Mendota Pool Bypass and Reach 2B Improvements Project
Project Description Technical Memorandum
October 2012
Table of Contents
1.0 Introduction ...... 1-1 1.1 Purpose of this TM ...... 1-1 1.2 Background ...... 1-1 1.2.1 Stipulation of Settlement...... 1-2 1.2.2 San Joaquin River Restoration Program ...... 1-4 1.2.3 Overview of the Mendota Pool Bypass and Reach 2B Improvements ...... 1-6 1.2.4 Scoping and Public Involvement Process ...... 1-8 1.3 Purpose and Uses of the Project EIS/R ...... 1-12 1.3.1 National Environmental Policy Act ...... 1-12 1.3.2 California Environmental Quality Act ...... 1-13 1.3.3 Type of Environmental Document...... 1-14 1.4 Relationship to Other SJRRP NEPA and CEQA Documents ...... 1-15 1.5 Purpose and Need for Action and Project Objectives ...... 1-16 1.6 Responsibilities of Lead Agencies, Responsible Agency, and Implementing Agencies ...... 1-17 1.7 Project Study Area ...... 1-18 1.7.1 Geographic Area Description ...... 1-18 1.7.2 Description of Existing Conditions within the Study Area ...... 1-18 1.7.3 Description of Local Hydrology ...... 1-24 1.8 Organization of this Technical Memorandum ...... 1-26
2.0 Alternatives Formulation Process ...... 2-1 2.1 Alternatives Development Process Overview ...... 2-1 2.2 Stakeholder Involvement ...... 2-2 2.2.1 Federal, State, & Local Agencies ...... 2-2 2.2.2 Landowners ...... 2-4 2.2.3 Public ...... 2-5 2.3 Initial Options Formulation ...... 2-5 2.4 Alternatives Formulation ...... 2-6 2.5 Summary of the Alternatives Evaluation Process ...... 2-8 2.5.1 Summary of the Evaluation Criteria ...... 2-8 2.5.2 Scoring Alternatives Data and Professional Judgment ...... 2-10
3.0 Description of Alternatives ...... 3-1 3.1 Alternatives Development ...... 3-1
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum i – October 2012 San Joaquin River Restoration Program
3.1.1 NEPA Requirements ...... 3-1 3.1.2 CEQA Requirements ...... 3-1 3.2 Overview of Alternatives ...... 3-2 3.3 No-Action/No-Project Alternative...... 3-3 3.4 Elements Common to All Action Alternatives ...... 3-5 3.4.1 Fish Habitat and Passage ...... 3-5 3.4.2 Levees ...... 3-8 3.4.3 Seepage Control Measures ...... 3-9 3.4.4 Borrow ...... 3-9 3.4.5 Levee protection...... 3-10 3.4.6 Removal of existing levees ...... 3-10 3.4.7 Floodplain Grading ...... 3-10 3.4.8 Lone Willow Slough Fish Screen ...... 3-11 3.4.9 Infrastructure for Fish Monitoring ...... 3-11 3.4.10 Existing infrastructure relocations or floodproofing...... 3-11 3.4.11 Construction Access...... 3-15 3.4.12 Operations and Maintenance...... 3-17 3.4.13 Land Acquisition ...... 3-20 3.4.14 Phased Implementation ...... 3-20 3.4.15 Monitoring and Management Plan...... 3-20 3.4.16 Conservation Strategy ...... 3-21 3.5 Compact Bypass with Narrow Floodplain and South Canal ...... 3-45 3.5.1 Fish Habitat and Passage ...... 3-48 3.5.2 Floodplain and Riparian Habitat ...... 3-49 3.5.3 Compact Bypass Channel ...... 3-51 3.5.4 South Canal ...... 3-51 3.5.5 Structures ...... 3-52 3.5.6 Water Deliveries ...... 3-57 3.5.7 Construction Considerations ...... 3-57 3.5.8 Summary ...... 3-58 3.6 Compact Bypass with Wide Floodplain and Bifurcation Structure...... 3-62 3.6.1 Fish Habitat and Passage ...... 3-65 3.6.2 Floodplain and Riparian Habitat ...... 3-66 3.6.3 Compact Bypass Channel ...... 3-69 3.6.4 Structures ...... 3-69 3.6.5 Water Deliveries ...... 3-70 3.6.6 Construction Considerations ...... 3-71 3.6.7 Summary ...... 3-71
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3.7 Fresno Slough Dam with Narrow Floodplain and Short Canal ...... 3-75 3.7.1 Fish Habitat and Passage ...... 3-78 3.7.2 Floodplain and Riparian Habitat ...... 3-79 3.7.3 Short Canal...... 3-79 3.7.4 Structures ...... 3-79 3.7.5 Removal of River Sediments ...... 3-83 3.7.6 Water Deliveries ...... 3-84 3.7.7 Construction Considerations ...... 3-84 3.7.8 Summary ...... 3-84 3.8 Fresno Slough Dam with Wide Floodplain and North Canal ...... 3-88 3.8.1 Fish Habitat and Passage ...... 3-91 3.8.2 Floodplain and Riparian Habitat ...... 3-92 3.8.3 North Canal ...... 3-92 3.8.4 Structures ...... 3-92 3.8.5 Removal of River Sediments ...... 3-93 3.8.6 Water Deliveries ...... 3-94 3.8.7 Construction Considerations ...... 3-94 3.8.8 Summary ...... 3-94 3.9 Alternatives Comparison Tables ...... 3-97
4.0 Alternatives Considered and Eliminated from Further Consideration ...... 4-1 4.1 Pre-Initial Options Analysis ...... 4-1 4.2 Pre-Evaluation Screening ...... 4-3 4.2.1 Bottomless Arch Culverts ...... 4-3 4.2.2 Corrugated Metal Pipe Culverts...... 4-4 4.2.3 Bridge ...... 4-4 4.2.4 Floodplain Vegetation Types ...... 4-4 4.2.5 Floodplain Recontouring ...... 4-4 4.2.6 Older Levee Setbacks ...... 4-4 4.2.7 Mendota Dam Removal ...... 4-4 4.2.8 Channel Grading from Reach 3 to Chowchilla Bifurcation Structure ...... 4-5 4.2.9 Floating Picket Weir ...... 4-5 4.2.10 Behavioral Barrier ...... 4-5 4.2.11 Velocity Barrier ...... 4-6 4.2.12 Other Types of Fish Screens ...... 4-6 4.2.13 Pump Diversion to Mendota Pool ...... 4-6 4.3 Initial Alternatives Screening ...... 4-7
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum iii – October 2012 San Joaquin River Restoration Program
5.0 Project Implementation ...... 5-1 5.1 Federal Actions ...... 5-6 5.1.1 U.S. Army Corps of Engineers Regulations ...... 5-6 5.1.2 Federal Endangered Species Act ...... 5-8 5.1.3 Fish and Wildlife Coordination Act ...... 5-10 5.1.4 National Historic Preservation Act, Section 106 ...... 5-10 5.1.5 Rivers and Harbors Act Section 9 and General Bridge Act of 1946...... 5-11 5.2 State Actions ...... 5-11 5.2.1 Clean Water Act Section 401 ...... 5-11 5.2.2 Clean Water Act Section 402 ...... 5-11 5.2.3 California Endangered Species Act ...... 5-12 5.2.4 California Fish and Game Code Section 1602 ...... 5-13 5.2.5 California Code of Regulations, Title 23 ...... 5-14 5.2.6 California Water Rights ...... 5-14 5.2.7 State Lands Commission Land Use Lease ...... 5-15 5.3 Local Actions ...... 5-15 5.3.1 San Joaquin Valley Air Pollution Control District Regulations ...... 5-15 5.3.2 Surface Mining and Reclamation Act of 1975 ...... 5-17 5.3.3 Williamson Act ...... 5-18 5.4 Applicable Laws, Policies, and Plans Not Requiring Specific Permit or Approval ...... 5-19 5.4.1 Federal...... 5-19 5.4.2 State...... 5-23 5.4.3 Local ...... 5-25
6.0 Acknowledgments ...... 6-1
7.0 References ...... 7-1
Tables
Table 1-1 Restoration and Water Management Framework in Key Settlement Paragraphs ...... 1-3 Table 1-2 Key Settlement Milestones ...... 1-6 Table 1-3 Compliance, Consultation, and Coordination to Be Supported by the Project EIS/R ...... 1-14 Table 3-1 Fish Passage Design Criteria ...... 3-7
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Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions...... 3-24 Table 3-3 Compact Bypass with Narrow Floodplain and South Canal Levees, Relocations, and Land Acquisition ...... 3-59 Table 3-4 Compact Bypass with Narrow Floodplain and South Canal Costs ...... 3-59 Table 3-5 Compact Bypass with Narrow Floodplain and South Canal Conditions and Features within the Project Boundary ...... 3-60 Table 3-6 Compact Bypass with Wide Floodplain and Bifurcation Structure Levees, Relocations, and Land Acquisition ...... 3-71 Table 3-7 Compact Bypass with Wide Floodplain and Bifurcation Structure Costs ...... 3-72 Table 3-8 Compact Bypass with Wide Floodplain and Bifurcation Structure Conditions and Features within the Project Boundary...... 3-73 Table 3-9 Fresno Slough Dam with Narrow Floodplain and Short Canal Levees, Relocations, and Land Acquisition ...... 3-85 Table 3-10 Fresno Slough Dam with Narrow Floodplain and Short Canal Costs ...... 3-85 Table 3-11 Fresno Slough Dam with Narrow Floodplain and Short Canal Conditions and Features within the Project Boundary ...... 3-86 Table 3-12 Fresno Slough Dam with Wide Floodplain and North Canal Levees, Relocations, and Land Acquisition ...... 3-94 Table 3-13 Fresno Slough Dam with Wide Floodplain and North Canal Costs ...... 3-95 Table 3-14 Fresno Slough Dam with Wide Floodplain and North Canal Conditions and Features within the Project Boundary ...... 3-96 Table 3-15 Levees, Relocations, and Land Acquisition ...... 3-98 Table 3-16 Costs ...... 3-99 Table 3-17 Conditions and Features within the Project Boundaries ...... 3-100 Table 5-1 Summary of Permits and Approvals Required for the Project ...... 5-2
Figures
Figure 1-1 Overview of the SJRRP Restoration Area and the Project Vicinity ...... 1-10 Figure 1-2 Mendota Pool Bypass and Reach 2B Channel Improvements Project Vicinity ...... 1-11 Figure 1-3 Reach 2B Channel prior to Interim Flows (12/15/09) ...... 1-19 Figure 1-4 View from downstream of the Chowchilla Bifurcation Structure in Reach 2B (12/15/09) ...... 1-21
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum v – October 2012 San Joaquin River Restoration Program
Figure 1-5 Inside of one of the bays at the Chowchilla Bifurcation Structure (12/15/09) ...... 1-21 Figure 1-6 Concrete sill and bordering riprap along the downstream edge of the Chowchilla Bifurcation Structure in Reach 2B (12/15/09) ...... 1-22 Figure 1-7 San Mateo Avenue Crossing of Reach 2B looking from north bank to south bank (12/15/09) ...... 1-23 Figure 1-8 San Mateo Avenue crossing of Reach 2B showing single culvert beneath the road (12/15/09) ...... 1-23 Figure 1-9 Downstream face of Mendota Dam (5/28/09) ...... 1-24 Figure 1-10 Restoration Flow hydrographs by restoration year type (Reach 2B) ...... 1-25 Figure 2-1 Alternatives Formulation Process ...... 2-2 Figure 2-2 Alternatives Formulation Process Diagram ...... 2-6 Figure 3-1 Example Floodplain Grading Approaches ...... 3-12 Figure 3-2 Existing Infrastructure in the Project Area ...... 3-13 Figure 3-3 Construction Access Routes...... 3-16 Figure 3-4 Plan View of Compact Bypass with Narrow Floodplain and South Canal ...... 3-46 Figure 3-5 Inset Map of Compact Bypass with Narrow Floodplain and South Canal ...... 3-47 Figure 3-6 Potential Inundation Acreage by Flow for Compact Bypass with Narrow Floodplain and South Canal ...... 3-48 Figure 3-7 Supplementary flow system plan-view diagram ...... 3-54 Figure 3-8 Plan View of Compact Bypass with Wide Floodplain and Bifurcation Structure ...... 3-63 Figure 3-9 Inset Map of Compact Bypass with Wide Floodplain and Bifurcation Structure ...... 3-64 Figure 3-10 Potential Inundation Acreage by Flow for Compact Bypass with Wide Floodplain and Bifurcation Structure...... 3-65 Figure 3-11 Typical distribution of vegetation alliances along a restored Reach 2B riparian bank section ...... 3-67 Figure 3-12 Plan View of Fresno Slough Dam with Narrow Floodplain and Short Canal...... 3-76 Figure 3-13 Inset Map of Fresno Slough Dam with Narrow Floodplain and Short Canal ...... 3-77 Figure 3-14 Potential Inundation Acreage by Flow for Fresno Slough Dam with Narrow Floodplain and Short Canal ...... 3-78 Figure 3-15 Plan View of Fresno Slough Dam with Wide Floodplain and North Canal ...... 3-89 Figure 3-16 Inset Map of Fresno Slough Dam with Wide Floodplain and North Canal ...... 3-90
Mendota Pool Bypass and Reach 2B Improvements Project vi – October 2012 Project Description Technical Memorandum Table of Contents
Figure 3-17 Potential Inundation Acreage by Flow for Fresno Slough Dam with Wide Floodplain and North Canal ...... 3-91
Attachments
Attachment A ...... Initial Alternatives Evaluation Attachment B ...... Evaluation Matrix
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum vii – October 2012 San Joaquin River Restoration Program
List of Abbreviations and Acronyms ACHP Advisory Council on Historic Preservation Act San Joaquin River Restoration Settlement Act AIA Air Impact Assessment CAA Clean Air Act CCAA California Clean Air Act CCID Central California Irrigation District CCR California Code of Regulations CDF California Department of Finance CEQ Council on Environmental Quality CEQA California Environmental Quality Act CESA California Endangered Species Act CFR Code of Federal Regulations cfs cubic feet per second CNPS California Native Plant Society Court U.S. Eastern District Court of California CRHR California Register of Historical Resources CVFED Central Valley Floodplain Evaluation and Delineation CVFPB Central Valley Flood Protection Board CVP Central Valley Project CVRWQCB Central Valley Regional Water Quality Control Board CWA Clean Water Act Delta Sacramento-San Joaquin Delta DFG California Department of Fish and Game DOE California Department of Water Resources, Division of Engineering DSOD California Department of Water Resources, Division of Safety of Dams DWR California Department of Water Resources EA Environmental Assessment EFH essential fish habitat EIS/R Environmental Impact Statement/Environmental Impact Report ESA Endangered Species Act Exchange Contractors San Joaquin River Exchange Contractors
Mendota Pool Bypass and Reach 2B Improvements Project viii – October 2012 Project Description Technical Memorandum Table of Contents
FONSI Finding of No Significant Impact Flood Control Project Lower San Joaquin River Flood Control Project Flood Operation Manual Flood Control Project’s Operation and Maintenance Manual for Levee, Irrigation and Drainage Structures, Channels and Miscellaneous Facilities fps feet per second FWCA Fish and Wildlife Coordination Act FWUA Friant Water Users Authority IS Initial Study ISMP Invasive Species Management Plan ISR Indirect Source Review Levee District Lower San Joaquin Levee District MBTA Migratory Bird Treaty Act MMRP Mitigation Monitoring and Reporting Program MND Mitigated Negative Declaration MOA Memorandum of Agreement MOU Memorandum of Understanding MSFCMA Magnuson-Stevens Fishery Conservation and Management Act NEPA National Environmental Policy Act NHPA National Historic Preservation Act NMFS National Marine Fisheries Service NOE Notice of Exemption NOI Notice of Intent NOP Notice of Preparation NRCS Natural Resources Conservation Service NRDC Natural Resources Defense Council NRHP National Register of Historic Places NWP Nationwide Permit OHV off-highway vehicle OHWM ordinary high water mark PEIS/R Program Environmental Impact Statement/ Environmental Impact Report Pool Mendota Pool PRC Public Resources Code PRD Permit Registration Documents Project Mendota Pool Bypass and Reach 2B Improvements Project
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum ix – October 2012 San Joaquin River Restoration Program
RA Restoration Administrator Reclamation U.S. Department of the Interior, Bureau of Reclamation Restoration Area the San Joaquin River Restoration area from Friant Dam to the Merced River confluence RHA Rivers and Harbors Act RM river mile RWA Recovered Water Account RWQCB Regional Water Quality Control Board Secretary Secretary of the U.S. Department of the Interior Settlement Stipulation of Settlement SHPO State Historic Preservation Officer SIP State Implementation Plan SJRRP San Joaquin River Restoration Program SMARA Surface Mining and Reclamation Act of 1975 State State of California SWP State Water Project SWPPP Storm Water Pollution Prevention Plan SWRCB State Water Resources Control Board TM Technical Memorandum USACE U.S. Army Corps of Engineers USC United States Code USEPA U.S. Environmental Protection Agency USFWS U.S. Fish and Wildlife Service USGS U.S. Geological Survey
Mendota Pool Bypass and Reach 2B Improvements Project x – October 2012 Project Description Technical Memorandum Table of Contents
Definitions For the purposes of the discussion in this technical memorandum, the following terms are defined.
The Project – The Project refers to the portion of Reach 2B that will convey Restoration Flows, the Mendota Pool Bypass, and all facilities related to implementation.
Reach 2B – Reach 2B refers either to the existing San Joaquin River between the Chowchilla Bifurcation Structure and the Mendota Dam or to the future portion of that reach which will contain Restoration Flows. Reach 2B does not include the Mendota Pool Bypass.
Mendota Pool Bypass – Refers to the portion of the Project (channels, structures, and other facilities) that will enable conveyance of Restoration Flows around the Mendota Pool.
Pre-appraisal level themes – Pre-appraisal level themes are concepts used in an iterative process of modeling coupled with public outreach and concept refinement. Themes were refined and presented as initial options in the Initial Options Technical Memorandum (TM) (SJRRP 2010e).
Initial Options – Initial options represent building blocks for future development of Project Alternatives. Initial options were prepared for each Project component and presented in the Initial Options TM as a “menu” of preliminary ideas to meet the Project goals for each component. The initial options were further refined into Initial Alternatives by subsequent data collection, analysis and analytical tools.
Initial Alternatives – Initial Alternatives are refined versions of the initial options and were used to conduct the alternatives evaluation presented here. The evaluation assesses the effects of the Initial Alternatives in several key resource areas (costs, schedule, fish habitat and passage, habitat restoration, geomorphology, economics, socioeconomics, land use, and threatened and endangered plants and wildlife). Initial Alternatives present a range of alternatives for each major component of the Project, both the Reach 2B improvements (Floodplain Initial Alternatives) and the Mendota Pool Bypass (Bypass Initial Alternatives).
Final Alternatives (Alternatives) – The Final Alternatives are those Floodplain Initial Alternatives and Bypass Initial Alternatives that were selected following the alternatives evaluation and paired to form a whole (complete) Project Alternative. They are presented in the Project Description TM as Alternatives, which will feed into the Environmental Impact Statement/Environmental Impact Report (EIS/R). Alternatives are of a sufficient detail to evaluate benefits and impacts, including Project costs, land acquisition, and
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum xi – October 2012 San Joaquin River Restoration Program mitigation needs. Each Alternative for the Project includes actions for both the Mendota Pool Bypass and the Reach 2B improvements.
Mendota Pool Bypass and Reach 2B Improvements Project xii – October 2012 Project Description Technical Memorandum Table of Contents
This Draft Technical Memorandum (TM) was prepared by the San Joaquin River Restoration Program (SJRRP) Team as a draft document in support of preparing an Environmental Impact Statement/Environmental Impact Report (EIS/R) for the Mendota Pool Bypass and Reach 2B Improvements Project (Project). The purpose for circulating this document at this time is to facilitate early coordination regarding initial approaches currently under consideration by the SJRRP Team with the Settling Parties, Third Parties, other stakeholders, and interested members of the public. Therefore, the content of this document may not necessarily be included in the Project EIS/R. While the SJRRP Team is not requesting formal comments on this document, comments received will be considered to the extent possible.
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Mendota Pool Bypass and Reach 2B Improvements Project xiv – October 2012 Project Description Technical Memorandum 1.0 Introduction This Project Description Technical Memorandum (TM) documents the process and results of the Draft and Final Alternatives formulation to implement the Mendota Pool Bypass and Reach 2B Improvements Project (Project), a component of Phase 1 of the overall San Joaquin River Restoration Program (SJRRP). The SJRRP was established in late 2006 to implement the Stipulation of Settlement (Settlement) in Natural Resources Defense Council (NRDC), et al,. v. Kirk Rodgers, et al.
The U.S. Department of the Interior, Bureau of Reclamation (Reclamation), as the Federal lead agency under the National Environmental Policy Act (NEPA), and the California Department of Water Resources (DWR), as the State lead agency under the California Environmental Quality Act (CEQA), prepared this TM as an initial step in preparation of an Environmental Impact Statement/ Environmental Impact Report (EIS/R) for the Project. Federal authorization for implementing the Settlement is provided in the San Joaquin River Restoration Settlement Act (Act) (Public Law 111-11).
1.1 Purpose of this TM
This TM is intended to:
• Explain the purpose and need of the Project • Define the Project study area • Describe the No-Action/No-Project Alternative • Describe the Action/Project Alternatives to be evaluated in the Project EIS/R • Document the alternatives formulation process • Document the alternatives evaluation methods and results • Serve as the basis for future discussions with the Implementing Agencies, Technical Work Groups, landowners, and other stakeholders involved in the Project
1.2 Background
Originating high in the Sierra Nevada Mountains, the San Joaquin River carries snowmelt from mountain meadows to the valley floor before turning north and becoming the backbone of tributaries draining into the San Joaquin Valley. The San Joaquin River is California’s second longest river and discharges to the Sacramento-San Joaquin Delta (Delta) and, ultimately, to the Pacific Ocean through San Francisco Bay.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-1 – October 2012 San Joaquin River Restoration Program
Historically, the San Joaquin River supported a rich and diverse ecosystem influenced by seasonal runoff patterns. During winter and spring months, runoff from Sierra Nevada streams would spread over the valley floor and slowly drain to the Delta, providing rich habitat supporting numerous aquatic and wildlife species, including Chinook salmon.
Over the past two centuries, development of water resources transformed the San Joaquin River. In the late 1880s, settlers in the Central Valley drained large areas of valley floor lands and put these lands into agricultural production, supported by small and seasonal diversion dams on the river and a series of water conveyance and drainage canals. Hydroelectric project development in the upper portions of the San Joaquin River watershed harnessed power from the river and modified the natural flow patterns.
In 1944, Reclamation completed construction of Friant Dam on the San Joaquin River. With the completion of Friant-Kern Canal in 1951 and Madera Canal in 1945, Friant Dam diverted San Joaquin River water supplies to over 1 million acres of highly productive farmland along the eastern portion of the San Joaquin Valley. Operation of the dam ceased flow in some portions of the river and extirpated salmon runs in the San Joaquin River upstream from the confluence with the Merced River.
1.2.1 Stipulation of Settlement In 1988, a coalition of environmental groups, led by the Natural Resources Defense Council (NRDC) filed a lawsuit, known as NRDC, et al., v. Kirk Rodgers, et al., challenging the renewal of long-term water service contracts between the United States and the Central Valley Project (CVP) Friant Division contractors. On September 13, 2006, after more than 18 years of litigation, the Settling Parties, including NRDC, Friant Water Users Authority (FWUA), and the U.S. Departments of the Interior and Commerce, agreed on the terms and conditions of a Settlement subsequently approved by the U.S. Eastern District Court of California (Court) on October 23, 2006. The San Joaquin River Restoration Settlement Act (Act), included in Public Law 111-11 and signed into law on March 30, 2009, authorizes and directs the Secretary of the Interior (Secretary) to implement the Settlement. The Settlement establishes two primary goals:
• Restoration Goal – To restore and maintain fish populations in “good condition” in the main stem San Joaquin River below Friant Dam to the confluence of the Merced River, including naturally reproducing and self-sustaining populations of salmon and other fish • Water Management Goal – To reduce or avoid adverse water supply impacts on all of the Friant Division long-term contractors that may result from the Interim and Restoration flows provided for in the Settlement To achieve the Restoration Goal, the Settlement calls for releases of water from Friant Dam to the confluence of the Merced River (referred to as Interim and Restoration flows), a combination of channel and structural modifications along the San Joaquin River below Friant Dam, and reintroduction of Chinook salmon. Restoration Flows are specific volumes of water to be released from Friant Dam during different year types, according to Exhibit B of the Settlement; Interim Flows are experimental flows that began in 2009 and will continue until full Restoration Flows are initiated, with the
Mendota Pool Bypass and Reach 2B Improvements Project 1-2 – October 2012 Project Description Technical Memorandum 1.0 Introduction
purpose of collecting relevant data concerning flows, temperatures, fish needs, seepage losses, recirculation, recapture, and reuse. To achieve the Water Management Goal, the Settlement calls for recirculation, recapture, reuse, exchange or transfer of the Interim and Restoration flows to reduce or avoid impacts to water deliveries to all of the Friant Division long-term contractors caused by the Interim and Restoration flows. In addition, the Settlement establishes a Recovered Water Account (RWA) and program to make water available to all of the Friant Division long-term contractors who provide water to meet Interim or Restoration flows to reduce or avoid the impact of the Interim and Restoration flows on such contractors.
The Settlement and the Act authorize and direct specific physical and operational actions that could potentially directly or indirectly affect environmental conditions in the Central Valley. Areas potentially affected by Settlement actions include the San Joaquin River and associated flood bypass system, tributaries to the San Joaquin River, the Delta, and water service areas of the CVP and State Water Project (SWP), including the Friant Division. Settlement Paragraphs 11 through 16 describe physical and operational actions (see Table 1-1).
Table 1-1 Restoration and Water Management Framework in Key Settlement Paragraphs Settlement Description of Constraint or Assumption Paragraph Identifies specific channel and structural improvements considered necessary to achieve the 11 Restoration Goal. Includes a reach-by-reach list of improvements. Acknowledges that additional channel or structural improvements not identified in 12 Paragraph 11 may be needed to achieve the Restoration Goal. Identifies specific volumes of water to be released from Friant Dam during different year- types (Restoration Flows), and provisional water supplies to meet the Restoration Flow 13 targets as provided in Exhibit B of the Settlement. Stipulates the release of full Restoration Flows no later than January 1, 2014, subject to then-existing channel capacities. Stipulates that spring-run and fall-run Chinook salmon be reintroduced to the San Joaquin River between Friant Dam and the confluence of the San Joaquin River with the Merced 14 River no later than December 31, 2012, consistent with all applicable law and after commencement of sufficient flows and the issuance of all necessary permits. Assigns priority to wild spring-run Chinook salmon over fall-run Chinook salmon. Specifies that Interim Flows begin no later than October 1, 2009, and continue until full 15 Restoration Flows can begin, to collect relevant data concerning flows, temperatures, fish needs, seepage losses, recirculation, recapture, and reuse. Requires that the Secretary of the Interior develop and implement a plan for recirculation, recapture, reuse, exchange, or transfer of the Interim and Restoration flows to reduce or 16 avoid impacts to water deliveries for all Friant Division long-term contractors. This paragraph also calls for establishment of an RWA and program to make water available to the Friant Division long-term contractors who provide water to meet Interim or Restoration flows. Key: CEQA = California Environmental Quality Act NEPA = National Environmental Policy Act PEIS/R = Program Environmental Impact Statement/Environmental Impact Report RWA = Recovered Water Account
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-3 – October 2012 San Joaquin River Restoration Program
1.2.2 San Joaquin River Restoration Program The SJRRP comprises several Federal and State of California (State) agencies responsible for implementing the Settlement. Implementing Agencies include: Reclamation, U.S. Fish and Wildlife Service (USFWS), National Marine Fisheries Service (NMFS), DWR, and California Department of Fish and Game (DFG). Exhibit C of the Settlement set forth milestone dates for the purposes of implementing the Settlement. The Implementing Agencies acknowledge that some of the implementation, including this project, is unavoidably behind schedule and have developed an Implementation Framework with a revised schedule (Third Party Working Draft Framework for Implementation (SJRRP 2012)). In addition, the Settlement stipulates that a Technical Advisory Committee be established, comprising six members appointed by NRDC and FWA. The Settlement also calls for a Restoration Administrator (RA) to be appointed by NRDC and FWA, to facilitate the Technical Advisory Committee and provide specific recommendations to the Secretary in coordination with the Technical Advisory Committee. The RA’s duties are defined in the Settlement, and include making recommendations to the Secretary on the release of Interim and Restoration flows. The RA is also responsible for consulting with the Secretary on implementing actions under Paragraph 11 of the Settlement, and for identifying and recommending additional actions under Paragraph 12 of the Settlement. In addition, the RA is responsible for consulting with the Secretary on the reintroduction of Chinook salmon under Paragraph 14 of the Settlement. The Secretary will diligently pursue completion of project-specific actions in consultation with the RA.
Mendota Pool Bypass and Reach 2B Improvements Project 1-4 – October 2012 Project Description Technical Memorandum 1.0 Introduction
Table 1-2 shows milestone dates recommended in the Settlement. The Implementing Agencies aim to achieve these milestones, as demonstrated by the release of Interim Flows beginning in October 2009; however, these dates may change, pending completion of compliance, coordination, consultation, data collection, and related efforts. Reclamation and DWR initiated the NEPA and CEQA processes in August 2007 to analyze implementation of the Settlement. Reclamation is the lead NEPA agency and DWR is the lead CEQA agency in preparing the Project EIS/R.
In addition, the Settlement stipulates that a Technical Advisory Committee be established, comprising six members appointed by NRDC and FWA. The Settlement also calls for a Restoration Administrator (RA) to be appointed by NRDC and FWA, to facilitate the Technical Advisory Committee and provide specific recommendations to the Secretary in coordination with the Technical Advisory Committee. The RA’s duties are defined in the Settlement, and include making recommendations to the Secretary on the release of Interim and Restoration flows. The RA is also responsible for consulting with the Secretary on implementing actions under Paragraph 11 of the Settlement, and for identifying and recommending additional actions under Paragraph 12 of the Settlement. In addition, the RA is responsible for consulting with the Secretary on the reintroduction of Chinook salmon under Paragraph 14 of the Settlement. The Secretary will diligently pursue completion of project-specific actions in consultation with the RA.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-5 – October 2012 San Joaquin River Restoration Program
Table 1-2 Key Settlement Milestones 1 Date Milestone Status October 2009 Initiate Interim Flows and Monitoring Program Completed September 2010 USFWS submits a completed permit application to Completed NMFS for reintroduction of spring-run Chinook salmon April 2012 NMFS issues a decision on the permit application for Future reintroduction of spring-run Chinook salmon December 2012 Reintroduce spring-run and fall-run Chinook salmon, if Future permitted by NMFS December 2013 Complete Phase 1 improvements identified in the Future Settlement Secretary of the Interior, in consultation with NRDC and FWA, develops operational guidelines January 2014 Initiate full Restoration Flows Future December 2016 Complete Phase 2 improvements identified in the Future Settlement December 2024 Secretary of Commerce reports to Congress on the Future progress made in reintroducing spring-run and fall-run Chinook salmon and discusses plans for future implementation of the Settlement December 2025 Review and revise Restoration Flows, if necessary Future January – July 2026 Any party to the Settlement may file a motion to request Future an increase, decrease, or material change in the quantity and/or timing of Restoration Flows Note: 1 These milestones are set forth in the Settlement. Key: FWA = Friant Water Authority NMFS = National Marine Fisheries Service NRDC = Natural Resources Defense Council Settlement = Stipulation of Settlement USFWS = U.S. Fish and Wildlife Service
1.2.3 Overview of the Mendota Pool Bypass and Reach 2B Improvements The Mendota Pool Bypass and Reach 2B Improvements Project (Project) includes the construction, operation, and maintenance of the Mendota Pool Bypass and improvements in the San Joaquin River channel in Reach 2B to convey at least 4,500 cubic feet per second (cfs). The Project area (Figure 1-1 and Figure 1-2) extends from approximately 0.3 miles above the Chowchilla Bypass Bifurcation Structure to approximately 1.0 mile below the Mendota Dam. It comprises the area that could be directly affected by the Project. The Project may also indirectly affect nearby portions of Reach 2A and Reach 3. The Project area is in Fresno and Madera counties, near the town of Mendota, California.
The Mendota Pool Bypass and Reach 2B improvements defined in the Settlement are (Settlement Paragraph 11(a)):
Mendota Pool Bypass and Reach 2B Improvements Project 1-6 – October 2012 Project Description Technical Memorandum 1.0 Introduction
(1) Creation of a bypass channel around Mendota Pool to ensure conveyance of at least 4,500 cfs from Reach 2B downstream to Reach 3. This improvement requires construction of a structure capable of directing flow down the bypass and allowing the Secretary to make deliveries of San Joaquin River water into Mendota Pool when necessary;
(2) Modifications in channel capacity (incorporating new floodplain and related riparian habitat) to ensure conveyance of at least 4,500 cfs in Reach 2B between the Chowchilla Bifurcation Structure and the new Mendota Pool bypass channel.
Because the functions of these channels may be inter-related, the design, environmental compliance, and construction of the two are being addressed as one project. The Project shall be implemented consistent with the Settlement and the San Joaquin River Restoration Settlement Act, Public Law 111-11, with implementation dates clarified by the Implementation Framework (SJRRP 2012).
The Mendota Pool Bypass would include conveying at least 4,500 cfs around the Pool from Reach 2B to Reach 3 and a fish barrier to direct upmigrating adult salmon into the bypass. The bypass could be accomplished by constructing a new channel around Mendota Pool or by limiting Mendota Pool to areas outside of the San Joaquin River. This action would include the ability to divert 2,500 cfs to the Pool and may consist of a bifurcation structure in Reach 2B. The bifurcation structure would include a fish passage facility to enable up-migrating salmon to pass the structure and a fish screen to direct out- migrating fish into the bypass channel and minimize or avoid fish entrainment to the Pool.
Improvements to Reach 2B would include modifications to the San Joaquin River channel from the Chowchilla Bypass Bifurcation Structure to the new Mendota Pool Bypass to provide a capacity of at least 4,500 cfs with integrated floodplain habitat. The options under consideration include potential levee setbacks along Reach 2B to increase the channel and floodplain capacity and provide for floodplain habitat. Floodplain habitat is included along the Reach 2B portion of the Project as required by the Settlement; floodplain habitat is being considered along the Mendota Pool Bypass channel because Central Valley floodplains have been shown to be of value to rearing juvenile salmon as they migrate downstream (Jeffres 2008, Grosholz 2006, Sommer 2004, Sommer 2001). In addition, the SJRRP Fisheries Management Plan (SJRRP 2010) describes that sufficient floodplain habitat is an important feature for meeting salmon population targets.
Improvements included in the project could potentially be implemented in a phased approach to facilitate scheduling and funding. Phased implementation is discussed further in Section 3.4.14.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-7 – October 2012 San Joaquin River Restoration Program
1.2.4 Scoping and Public Involvement Process The Implementing Agencies conducted public and stakeholder outreach activities to engage and inform all interested parties of Project activities. Engaging those interested parties helped to inform the process for scoping the Project Alternatives, including development of this Project Description TM. Reclamation initiated the NEPA process by issuing a Notice of Intent (NOI) on July 13, 2009, and DWR initiated the CEQA process by issuing a Notice of Preparation (NOP) on the same day, to prepare a Project EIS/R and hold public scoping meetings. The Project EIS/R scoping comment period began the date the NOI was issued and ended on August 14, 2009. The Implementing Agencies convened two public meetings, one each in Fresno (July 28, 2009) and Firebaugh (July 29, 2009), to inform the public and interested stakeholders about the Project, and to solicit comments and input on the scope of the EIS/R. Reclamation and DWR received comments from 29 entities, including Federal and State agencies, local interest groups, local residents, farmers, landowners, public advocacy groups, and individuals. The comments received were summarized in a Public Scoping Report released February 2010 (SJRRP 2010c). The NEPA scoping process also serves as the scoping process for compliance with other Federal laws such as the National Historic Preservation Act, Section 106.
Public involvement and outreach activities have enabled the Implementing Agencies to involve stakeholders and incorporate public and stakeholder input into the development of major Project documents, including this Project Description TM. These activities seek to create an open and transparent process through which the general public, stakeholders, affected Third Parties, and other interested parties can track and participate in SJRRP activities, including the formulation of alternatives for this Project Description TM. Ongoing public outreach activities conducted in support of the Project include the following:
• Hosting Project-specific landowner meetings as well as participating in SJRRP Technical Feedback Meetings with subject-matter experts, Settling Parties, affected stakeholders, and the general public to obtain information and viewpoints from individual attendees; provide updates on the status of Project work products; keep the Technical Feedback Group up-to-date with the current status of the Project; gather feedback on Project documents; and discuss potential opportunities and constraints that may arise. The format of obtaining and disseminating information through the landowner meetings and Technical Feedback Group meetings is intended to be flexible to address the issues and documents at hand and to accommodate the needs of the SJRRP, Settling Parties, stakeholders, and the general public. • Making available technical memoranda and other milestone Project documents to the general public, stakeholders, affected Third Parties, and other interested parties on the SJRRP Web site. The lead agency must, whenever practicable, use a consensus-based management approach to the NEPA process, as required by 43 CFR 46.110. Consensus-based management “…involves outreach to persons, organizations or communities who may be interested in or affected by a proposed action with an assurance that their input will be
Mendota Pool Bypass and Reach 2B Improvements Project 1-8 – October 2012 Project Description Technical Memorandum 1.0 Introduction
given consideration by the Responsible Official in selecting a course of action” (43 CFR 46.110(a)). The Project Description TM was developed with a consensus-based management approach. The completed and ongoing activities conducted in support of the Project, as described above, constitute outreach performed in support of this approach.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-9 – October 2012 San Joaquin River Restoration Program
Project Vicinity
Figure 1-1 Overview of the SJRRP Restoration Area and the Project Vicinity
Mendota Pool Bypass and Reach 2B Improvements Project 1-10 – October 2012 Project Description Technical Memorandum 1.0 Introduction
Figure 1-2 Mendota Pool Bypass and Reach 2B Channel Improvements Project Vicinity
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-11 – October 2012 San Joaquin River Restoration Program
1.3 Purpose and Uses of the Project EIS/R
The purpose of the Draft Project EIS/R will be to analyze the project-specific direct, indirect, and cumulative impacts of implementing the Project as directed by the Act, consistent with NEPA/CEQA requirements. The Draft Project EIS/R will serve as an informational document for decision makers, public agencies, non-government organizations, and the general public regarding the potential direct and indirect environmental consequences of implementing any of the alternatives.
The Draft Project EIS/R will not identify a preferred alternative for implementation. Consistent with CEQ Regulations, 40 CFR Part 46.425, and State CEQA Guidelines, the Final Project EIS/R will identify a preferred alternative for implementation (or alternatives, if more than one exists). The preferred alternative will be identified in the Final Project EIS/R based on the information presented in this Draft Project EIS/R, in light of any potential revisions made in response to comments received on the Draft Project EIS/R. After the Final Project EIS/R is published, Reclamation will prepare and adopt a Record of Decision, and DWR will prepare and adopt a Notice of Determination, to implement the preferred alternative.
1.3.1 National Environmental Policy Act NEPA provides an interdisciplinary framework for Federal agencies to take environmental factors into account during a decision making process (42 United States Code (USC) 4321, 40 CFR 1500.1). NEPA requires an Environmental Impact Statement (EIS) whenever a proposed major Federal action (e.g., a proposal for legislation or an activity financed, assisted, conducted, or approved by a Federal agency with Federal agency control) significantly affects the quality of the human environment. Section 1508.14 of the CEQ Regulations defines the human environment to include “the natural and physical environment and the relationship of people with that environment.”
The EIS, in conjunction with other relevant material, is used by the Federal Government to plan actions and make decisions. Section 1502.1 of the CEQ Regulations states that an EIS primarily serves as an action-forcing device to infuse the policies and goals defined in NEPA into ongoing programs and actions of the Federal Government. As an informational document, an EIS provides a rigorous and objective evaluation of all reasonable alternatives; full and open disclosure of environmental consequences before agency action; an interdisciplinary approach to project evaluation; identification of measures to mitigate impacts; and an avenue for public and agency participation in decision making (40 CFR 1502.1). NEPA defines mitigation as avoiding, minimizing, rectifying, reducing, or compensating for significant effects of a proposed action (40 CFR 1508.20). NEPA also requires evaluating a proposed action and alternatives at an equal level of detail.
NEPA requires that a lead agency “include [in an EIS] appropriate mitigation measures not already included in the proposed action or alternatives” (40 CFR 1502.14(f)). An EIS must also include discussions of “means to mitigate adverse environmental impacts (if not fully covered under Section 1502.14(f)).” In preparing a Record of Decision under 40 CFR 1505.2, a lead agency must “[s]tate whether all practicable means to avoid or
Mendota Pool Bypass and Reach 2B Improvements Project 1-12 – October 2012 Project Description Technical Memorandum 1.0 Introduction
minimize environmental harm from the alternative selected have been adopted, and if not, why they were not. A monitoring and enforcement program shall be adopted and summarized where applicable for any mitigation.”
1.3.2 California Environmental Quality Act The State CEQA Guidelines (14 CCR Section 15064(f)(1)) require that an Environmental Impact Report (EIR) be prepared whenever a project may result in a significant environmental impact. Section 15064(d) states that “in evaluating the significance of the environmental effect of a project, the lead agency shall consider direct physical changes in the environment which may be caused by the project and reasonably foreseeable indirect physical changes in the environment which may be caused by the project.” An EIR is an informational document used to inform public agency decision makers and the general public of the significant environmental effects of a project, identify possible ways to mitigate or avoid the significant effects, and describe a range of reasonable alternatives to the project that could feasibly attain most of the basic objectives of the project while substantially lessening or avoiding any of the significant environmental impacts. When determining whether to approve a project, State and local public agencies are required by CEQA to consider the information presented in the EIR.
CEQA requires that State and local government agencies consider the potential environmental effects of projects over which they have discretionary authority before taking action on those projects (Public Resources Code (PRC) Section 21000 et seq.). CEQA also requires that each public agency avoid or mitigate to less-than-significant levels, wherever feasible, the significant environmental effects of projects it approves or implements. If a project would result in significant and unavoidable environmental impacts that cannot be feasibly mitigated to less-than-significant levels, the project can still be approved, but the lead agency’s decision makers must issue a “statement of overriding considerations” explaining in writing the specific economic, social, or other considerations that they conclude, based on substantial evidence, make those significant effects acceptable.
Section 15126.6(a) of the State CEQA Guidelines also requires that an EIR describe and evaluate a reasonable range of alternatives that would feasibly attain most of the basic project objectives, and would avoid or substantially lessen any significant impact of the project, as proposed. A range of reasonable alternatives is analyzed to define issues and provide a clear basis for choice among options. CEQA requires that the lead agency consider alternatives that would avoid or reduce one or more of the significant impacts identified for a project in an EIR. The State CEQA Guidelines state that the range of alternatives required to be evaluated in an EIR is governed by the “rule of reason”; the EIR needs to describe and evaluate only those alternatives necessary to permit a reasonable choice and to foster informed decision making and informed public participation (Section 15126.6(f)). Consideration of alternatives focuses on those that can either eliminate significant adverse environmental impacts, or reduce them to less-than significant levels; alternatives considered in this context may include those that are more costly and those that could impede to some degree the attainment of all project objectives (Section 15126(b)). CEQA does not require alternatives to be evaluated in the same level of detail as the proposed project.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-13 – October 2012 San Joaquin River Restoration Program
1.3.3 Type of Environmental Document The Draft Project EIS/R, which this Project Description TM will become part of, will present project-level analyses of certain actions fully described in each alternative. Actions considered for evaluation but not included in the action alternatives (described in Attachment A, “Alternatives Evaluation”) are not prohibited from future implementation, but would require separate analysis pursuant to NEPA and/or CEQA at a project level of detail.
Compliance and Permits Supported by the Project EIS/R The Project EIS/R will support the needed permits, petitions, and similar compliance, coordination, and consultation efforts for the Project actions, as shown in Table 1-3 and described in Section 5.0.
Table 1-3 Compliance, Consultation, and Coordination to Be Supported by the Project EIS/R Resource Laws/Regulations/Permits Regulating Agency/Agencies Applicable All San Joaquin River Restoration Settlement Act Secretary of the Interior Section 10 of the Rivers and Harbors Act – U.S. Army Corps of Engineers Individual or General Permit Section 401 of the Clean Water Act – Water Regional Water Quality Control Board Quality Certification or Waiver Section 402 of the Clean Water Act – National State Water Resources Control Board Wetlands and Pollutant Discharge Elimination System and Regional Water Quality Control Waters permit(s) Board Section 404 of the Clean Water Act – Individual U.S. Army Corps of Engineers or General Permit Sections 1600 through 1607 of the California California Department of Fish and Game Fish and Game Code – Streambed Alteration Agreement Section 7 of the Federal Endangered Species U.S. Fish and Wildlife Service and Federally Listed Act – Section 7 Consultation National Marine Fisheries Service Species Section 10(j) of the Federal Endangered National Marine Fisheries Service Species Act – Section 10 permit Magnuson-Stevens Fishery Conservation and National Marine Fisheries Service Management Act Fish and Wildlife Fish and Wildlife Coordination Act report U.S. Fish and Wildlife Service Resources Migratory Bird Treaty Act U.S Fish and Wildlife Service Bald and Golden Eagle Protection Act U.S Fish and Wildlife Service National Historic Preservation Act – Section State Office of Historic Preservation Cultural Resources 106 Consultation
Mendota Pool Bypass and Reach 2B Improvements Project 1-14 – October 2012 Project Description Technical Memorandum 1.0 Introduction
Table 1-3 Compliance, Consultation, and Coordination to Be Supported by the Project EIS/R Resource Laws/Regulations/Permits Regulating Agency/Agencies Applicable
State-Listed Sections 2080.1 and 2081 of the California California Department of Fish and Game Species/State Endangered Species Act – Consistency Special-Status Determination/Incidental Take Permit Species California Native Plant Protection Act California Department of Fish and Game Section 14 of the Rivers and Harbors Act U.S. Army Corps of Engineers (“Section 408”) – Permission Levees and Central Valley Flood Protection Board Central Valley Flood Protection Board Floodways Encroachment Permit and 33 Code of Federal and U.S. Army Corps of Engineers Regulations 208.10 (U.S. Army Corps of Engineers review) Section 9 of the Rivers and Harbors Act and U.S Coast Guard Bridges General Bridge Act of 1946 permit Porter-Cologne Water Quality Control Act and Regional Water Quality Control Board Water Quality Basin Plan for the Sacramento River & San Joaquin River Basins California Water Code – Water Right Petitions State Water Resources Control Board Water Rights (including petitions for changes to Water Right Permits 11885, 11886, and 11887) State Lands Land Use Lease State Lands Commission Authority to Construct, Permit to Operate San Joaquin Valley Air Pollution Control Air Quality District Program State-Owned Encroachment Permit California Department of Transportation Roadways California Surface Mining and Reclamation Act California Surface Mining and Surface Mining permit Reclamation Act lead agencies and California Department of Conservation
1.4 Relationship to Other SJRRP NEPA and CEQA Documents
Several environmental documents have been prepared previously to facilitate early actions needed to implement the Settlement. These documents include the following:
• Installation and Rehabilitation of Stream Gages on the San Joaquin River, Fresno, Madera, and Merced Counties, California Environmental Assessment (EA)/Finding of No Significant Impact (FONSI). Reclamation. December 2008. • San Joaquin River Restoration Program Water Level Recorder Installation and Data Collection Notice of Exemption (NOE). DWR. February 2009. • San Joaquin River Restoration Program Scour Chain Installation and Data Collection NOE. DWR. February 2009.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-15 – October 2012 San Joaquin River Restoration Program
• Stream Gage Installation and Operation and Maintenance Project Initial Study (IS)/Mitigated Negative Declaration (MND). DWR. March 2009. • San Joaquin River Restoration Program Stream Bed and Sand Sampling NOE. DWR. April 2009. • Chowchilla Bifurcation Structure Gate Seal Installation NOE. DWR. August 2009. • Interim Flows Project – Water Year 2010 Final EA/FONSI and IS/MND. Reclamation and DWR. September 2009. • Draft San Joaquin River Restoration Program Geotechnical Investigation and Seepage Well Installation Project IS/MND. DWR. October 2009 • Interim Flows Project – Water Year 2011 Final Supplemental EA/FONSI. Reclamation. September 2010. • Draft San Joaquin River Restoration Program PEIS/R. April 2011. • Recirculation of Recaptured Water Year 2011 San Joaquin River Restoration Program Interim Flows Final EA. May 2011. • Friant-Kern Canal Capacity Restoration Draft EA/FONSI. June 2011 • Interim Flows Project – Water Year 2012 Draft Supplemental EA/FONSI. Reclamation. June 2011.
1.5 Purpose and Need for Action and Project Objectives
NEPA regulations require a statement of “the underlying purpose and need to which the agency is responding in proposing the alternatives, including the Proposed Action” (40 CFR 1502.13). The State of California (State) CEQA Guidelines require a clearly written statement of objectives, including the underlying purpose of a project (Guidelines Section 15124(b)).
The purpose of the Proposed Action is to implement portions of the Settlement consistent with the Act. The Act authorizes and directs the Secretary to implement the Settlement. Specifically, this Project is intended to implement Paragraphs 11(a)(1) and 11(a)(2) of the Settlement, which are authorized in Sec. 10004.(a)(1) of the Act.
The Settlement specifies the need, which requires modifications to Reach 2B and construction of a bypass around Mendota Pool in support of achieving the Restoration Goal (Settlement Paragraph 2):
… a goal of this Settlement is to restore and maintain fish populations in “good condition” in the main stem of the San Joaquin River below Friant Dam to the confluence of the Merced River, including naturally-reproducing and self-sustaining populations of salmon and other fish (the “Restoration Goal”).
Mendota Pool Bypass and Reach 2B Improvements Project 1-16 – October 2012 Project Description Technical Memorandum 1.0 Introduction
The objectives of the proposed action are identified in Paragraphs 11(a)(1) and 11(a)(2) of the Settlement:
Paragraph 11(a)(1)
Creation of a bypass channel around Mendota Pool to ensure conveyance of at least 4,500 cfs from Reach 2B downstream to Reach 3. This improvement requires construction of a structure capable of directing flow down the bypass and allowing the Secretary to make deliveries of San Joaquin River water into Mendota Pool when necessary;
Paragraph 11(a)(2)
Modifications in channel capacity (incorporating new floodplain and related riparian habitat) to ensure conveyance of at least 4,500 cfs in Reach 2B between the Chowchilla Bifurcation Structure and the new Mendota Pool bypass Channel;
The purpose and objectives respond to a need to provide increased capacity and floodplain and riparian habitat in Reach 2B, as well as fish passage and rearing habitat.
1.6 Responsibilities of Lead Agencies, Responsible Agency, and Implementing Agencies
Reclamation is the lead NEPA agency and DWR is the lead CEQA agency in preparing this Project Description TM. The actions identified in the Project Description TM include actions to be undertaken by Reclamation and DWR, and other implementing parties. The effects of these actions are to be identified in the Project EIS/R.
The Implementing Agencies include Reclamation, USFWS, NMFS, DWR, and DFG. The Settlement identifies the Secretary as the lead Federal entity responsible for implementation and USFWS as the lead Federal agency responsible for reintroduction of spring-run and fall-run Chinook salmon. The Settlement also identifies the Secretary of the U.S. Department of Commerce, through NMFS, as a necessary participant to allow for permitting the reintroduction of spring-run Chinook salmon. The Act authorizes and directs the Secretary to implement the Settlement and appropriates funds for implementation. Implementation of the Settlement also requires involvement of the State’s Natural Resources Agency through DWR and DFG. Consistent with a Memorandum of Understanding (MOU) between the Settling Parties and the State, the California Natural Resources Agency will play a major role in funding and implementing actions called for in the Settlement and in the Act. DWR will assist in planning, designing, and constructing the physical improvements identified in the Settlement, including projects related to flood protection, levee relocation, and modifications to and maintenance of channel facilities. DFG will provide technical assistance on actions related to the release of Interim and Restoration flows and the reintroduction and
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-17 – October 2012 San Joaquin River Restoration Program
monitoring of fish, and planning, designing, and constructing facilities to provide fish passage. SWRCB, as a State agency, may take a discretionary action, in the form of a water rights approval related to the relocation of diversions. Additional information on responsible agencies and permit requirements is provided in Section 5.0.
1.7 Project Study Area
1.7.1 Geographic Area Description The study area for the Project, shown in Figure 1-2, (township 13S, range 15E) includes areas that may be affected directly or indirectly by implementing Project actions. The Project has two major components: Reach 2B and the Mendota Pool Bypass. Reach 2B generally includes the area from the San Joaquin River Control Structure near the Chowchilla Bypass downstream to Mendota Dam. Improvements in Reach 2B, which vary by Alternative, extend from the Chowchilla Bifurcation Structure on the upstream end to the head of the Mendota Pool Bypass channel or to Mendota Dam on the downstream end. However, Reach 2B improvements may also include areas just upstream of the Chowchilla Bifurcation Structure and may continue downstream of the head of the Mendota Pool Bypass or Mendota Dam, including the Pool area, as necessary to meet Project goals and objectives. The lateral extent of Reach 2B improvements, which varies by Alternative, includes lands to the north and south of the San Joaquin River in Reach 2B.
The Mendota Pool Bypass generally includes the area from the downstream end of the Reach 2B improvements to a tie-in location in Reach 3. Improvements for the Mendota Pool Bypass, which vary by Alternative, extend from the area south of Mowry Bridge over Fresno Slough to the area north of Mendota Dam where the Bypass ties into Reach 3. The Mendota Pool Bypass also includes areas adjacent to and on the west side of Mendota Pool and Fresno Slough and areas to the south of the Reach 2B improvements. Areas indirectly affected by this Project include the portions of Reach 3 to the downstream and Reach 2A to the upstream that are outside the study area.
The study area reflects current estimates of areas that may be affected by the Project Alternatives. In the Project EIS/R, the area where direct and indirect effects may occur differs according to resource area; therefore, the geographic range and environmental conditions that would be described in the Project EIS/R would vary by resource.
1.7.2 Description of Existing Conditions within the Study Area At the upstream end of the Project, the Chowchilla Bifurcation Structure is used to control and route flood releases from Friant Dam and the upstream watershed into Reach 2B and the Chowchilla Bypass, a flood protection project on the San Joaquin River. Under no-flow conditions, plunge pools (approximately 7 feet deep and 10 feet deep, respectively) can be observed at the downstream base of the Chowchilla Bifurcation Structure in both the San Joaquin River and the Chowchilla Bypass.
Reach 2B ends on the downstream end at the Mendota Dam, which creates Mendota Pool (Pool). The Delta Mendota Canal terminates at the Pool, which distributes water
Mendota Pool Bypass and Reach 2B Improvements Project 1-18 – October 2012 Project Description Technical Memorandum 1.0 Introduction
deliveries from the Delta to the San Joaquin River Exchange Contractors (Exchange Contractors) via the Main Canal, Helm Ditch, Columbia Canal, Main Lift Canal, and Outside Canal. The Pool is shallow with little storage volume, and the pool elevation is maintained for the purposes of hydraulic head into Fresno Slough. The Pool does not contain additional storage above the operating elevation and, therefore, does not provide substantial flood control protection. During flood releases, the flash boards are removed at Mendota Dam allowing the backwatered Pool to become part of the flowing river.
Flood flows through Mendota Pool are released from Friant Dam, Pine Flat Dam, or both. Friant Dam flood control releases may be diverted into Reach 2B at the Chowchilla Bifurcation Structure, and Pine Flat Dam flood control releases may be diverted into Mendota Pool via the James Bypass and Fresno Slough. Pine Flat Dam flood control releases have
priority over Friant Dam flood Figure 1-3 control releases, so depending Reach 2B Channel prior to Interim Flows on the available capacity in (12/15/09) Reach 3, a portion or all of the flow from Reach 2A may be diverted into the Chowchilla Bypass. Pine Flat Dam flood control releases into Mendota Pool occur in wet years (approximately 1 in 5 years). Accordingly during wet years, flow in Reach 2B may be reduced during flood control releases from Pine Flat Dam.
The Project study area includes only one existing private crossing, a dip-crossing at San Mateo Avenue, consisting of a culvert to convey low flows and an earthen embankment supporting the roadbed, which is overtopped during higher flows.
The San Mateo Avenue crossing is the approximate limits of the backwater effects of the Pool. Downstream of San Mateo Avenue, the river channel is inundated as a result of the Pool water surface elevation. Upstream of the crossing, the channel is only wetted during Interim Flows or flood releases from Friant Dam. The Pool and associated river channel are drained approximately every two years to inspect and perform maintenance on Mendota Dam.
Several water diversions (including Lone Willow Slough and the Columbia Canal), canals, lift stations, and groundwater wells exist within the Project area. Additionally, electrical and gas distribution lines and water pipelines lie within the Project area.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-19 – October 2012 San Joaquin River Restoration Program
Existing Land Use and Habitat A narrow corridor of riparian and aquatic habitat exists along the river corridor, levees, and at Mendota Pool; otherwise, land use within and surrounding the Project area is primarily agriculture with the exception of the water management facilities at the Pool.
The Pool backwater supports perennial riparian vegetation, predominantly willow riparian and cottonwood riparian forest communities with emergent wetland communities. Upstream of San Mateo Avenue and prior to Interim Flows, the channel exhibited a sandy substrate with little to no in-channel vegetation. Existing vegetation along the banks of the channel in these areas consists predominantly of riparian scrub and willow scrub communities.
Existing Fish Population and Habitat Conditions Prior to Interim Flows, Reach 2B upstream of San Mateo Avenue was dry except during flood flows (approximate frequency is every 5 years) consequently there are very limited in-channel habitat features. The Pool contains mostly introduced fishes and potentially a few native fish. The biannual dewatering of the Pool leaves the Pool site mostly dry, but some locations hold standing water during the several week period the Pool is drained in mid-winter.
The Reach 2B channel bed is composed of unconsolidated fine sand and there is little definition of the channel bed, which is typical for sand bed systems. No pool-bar structure or bed features occur which would typically be used in gravel bed or coarser systems to classify and evaluate fish habitat features (pools, riffles, runs) or conditions (instream cover, overhead cover, etc.).
Aquatic habitat in Reach 2B upstream of San Mateo Avenue is limited because there is a long history of the channel being dry prior to the start of Interim Flows. Riparian vegetation is limited to the levees along the channel banks. In the lower portion of Reach 2B, the channel is defined where vegetation has been established along the backwatered portion from the Pool between Mendota Dam and San Mateo Avenue. The Pool is bordered by emergent, wetland and riparian vegetation including mature cottonwood trees. Aquatic habitat in this section of river is affected by the backwatering of Mendota Dam and sedimentation in the Pool.
Existing Structures
Chowchilla Bifurcation Structure The most upstream structure is the Chowchilla Bifurcation Structure (Figure 1-2 and Figure 1-4). This structure is used to route flood flows in excess of water supply demands down the Chowchilla Bypass. The structure has wingwalls bounding four gated bays on each channel. The bays are essentially 20-foot wide by 18-foot high box culverts containing a trash rack on the upstream side (Figure 1-5). The four bays discharge across a row of energy dissipaters (dragons teeth) then over a concrete slab that is bounded on the downstream end by a 2-foot high concrete weir. Immediately below the concrete weir is a row of rip rap sitting against the concrete weir and above the sand bed of Reach 2B
Mendota Pool Bypass and Reach 2B Improvements Project 1-20 – October 2012 Project Description Technical Memorandum 1.0 Introduction
(Figure 1-6). Upstream and downstream of the structure, is the sand bed of Reach 2A and 2B, respectively.
Figure 1-4 View from downstream of the Chowchilla Bifurcation Structure in Reach 2B (12/15/09)
Figure 1-5 Inside of one of the bays at the Chowchilla Bifurcation Structure1 (12/15/09)
1 Ponded water shown in Figure 1-5 is the remains of the 2009 fall Interim Flows.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-21 – October 2012 San Joaquin River Restoration Program
Figure 1-6 Concrete sill and bordering riprap along the downstream edge of the Chowchilla Bifurcation Structure in Reach 2B2 (12/15/09)
San Mateo Avenue Crossing The present crossing of Reach 2B is a dip crossing or low-water crossing (Figure 1-7, Figure 1-8). Flows less than approximately 150 cfs are routed through a culvert beneath the road. At flows above approximately 150 cfs, the road is inundated (Houk 2009). The north (Madera County) portion of the crossing is within public right-of-way, but the south (Fresno County) portion of the crossing is on private land, essentially rendering it a private river crossing.
2 Ponded water shown in Figure 1-6 is the remains of the 2009 fall Interim Flows.
Mendota Pool Bypass and Reach 2B Improvements Project 1-22 – October 2012 Project Description Technical Memorandum 1.0 Introduction
Figure 1-7 San Mateo Avenue Crossing of Reach 2B looking from north bank to south bank (12/15/09)
Figure 1-8 San Mateo Avenue crossing of Reach 2B showing single culvert beneath the road (12/15/09)
Mendota Dam and Mendota Pool Mendota Dam (Figure 1-2 and Figure 1-9), at the downstream end of Reach 2B, forms a pool approximately 7 miles long to San Mateo Avenue. The downstream 2 to 3 miles of the channel is bordered by mature trees along the north bank. Typically, the Pool receives water from the Delta Mendota Canal which supplies water to the Helm Ditch, Main Canal, Outside Canal, Main Lift Canal, Fresno Slough, and Columbia Canal. The Pool is shallow and is drained about every two years for dam inspection and maintenance.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-23 – October 2012 San Joaquin River Restoration Program
Figure 1-9 Downstream face of Mendota Dam (5/28/09)
1.7.3 Description of Local Hydrology As part of the SJRRP, Restoration Flows will be released from Friant Dam based on water year type and other factors and conveyed to Reach 2B (see Figure 1-10). Flows conveyed into or diverted from Reach 2B and the Mendota Pool include:
• Restoration and Interim flows • Exchange Contractor deliveries to Mendota Pool from the San Joaquin River • Exchange Contractor deliveries to Mendota Pool from the Delta-Mendota Canal • Millerton Lake flood releases • Pine Flat Reservoir flood releases • Diversions to Mendota Pool via groundwater pump-ins • Diversions from Mendota Pool via the Columbia Canal, Mendota Dam (for Arroyo Canal in Reach 3), Helm Ditch, Main Canal, Outside Canal, Fresno County Waterworks District Canal, Fresno Slough, and Mowry pumps • Diversions from the river via Lone Willow Slough and other pumps for riparian rights diversions
Mendota Pool Bypass and Reach 2B Improvements Project 1-24 – October 2012 Project Description Technical Memorandum 1.0 Introduction
1 Hydrographs reflect assumptions about seepage losses and tributary inflows which are specified in the Settlement. 2 Reach 2B hydrographs are labeled as Reach 3 in Settlement Exhibit B. Figure 1-10 Restoration Flow hydrographs by restoration year type (Reach 2B)
With the SJRRP and the Reach 2B Project, there are three basic flow scenarios involving Restoration Flows, flood flows, and water deliveries that will typically occur in Reach 2B:
• In critical-low to normal-wet water year types, Restoration Flows will proceed through Reach 2B and irrigation deliveries and diversions will occur in Mendota Pool with no interaction between the Restoration Flows in Reach 2B and Mendota Pool. • In normal-wet to wet water year types, flood releases from Millerton Lake may be diverted from Reach 2B into the Chowchilla Bypass as well as to Mendota Pool where they can be used to fulfill water contracts or by legal water rights holders while alleviating pressure on the flood system. Some portion of these flows is anticipated to perform as Restoration Flows in Reach 2B, but the flood management agencies will have ultimate discretion in directing flood flows. • In wet water year types, flood releases from Pine Flat Reservoir may be bypassed to the San Joaquin River via Fresno Slough and Mendota Pool. Due to capacity restrictions downstream of Reach 2B, the addition of these flows further restricts the amount of flow that can enter Reach 2B, and more San Joaquin River flows will be diverted into the Chowchilla Bypass to compensate. Some portion of the
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 1-25 – October 2012 San Joaquin River Restoration Program
San Joaquin River flows is anticipated to perform as Restoration Flows in Reach 2B, but the flood management agencies will have ultimate discretion in directing flood flows.
In addition to the above flow scenarios, the SJRRP has the ability to manage Restoration Flows shown in Figure 1-10 in order to meet the Program’s goals and objectives. These management strategies include reshaping the flow block by moving it earlier in the schedule, later in the schedule, compressing the flow block, or extending it consistent with the provisions in the Settlement.
1.8 Organization of this Technical Memorandum
The content and format of this TM are intended to dovetail with the future Project EIS/R, which will meet the requirements of NEPA and CEQA. The TM is organized as shown below.
Executive Summary – summarizes Project purpose, study area, Alternatives, and stakeholder involvement. This section may be used as a stand-alone handout.
Section 1.0 Introduction – summarizes Project background and context, scope of this TM, Project purpose and need, Project study area, and TM organization.
Section 2.0 Alternatives Formulation Process – summarizes the process that was implemented to develop, evaluate, and select the Alternatives.
Section 3.0 Description of Alternatives – describes the Alternatives including the no- project/no-action alternative.
Section 4.0 Alternatives Considered and Eliminated from Further Consideration – describes options and alternatives that were considered throughout the alternatives formulation process but were eliminated from further consideration and the reasons for their elimination.
Section 5.0 Project Implementation – describes the State, Federal, and other agency actions (permits and approvals) required in order to implement the Project.
Section 6.0 Acknowledgments – provides a list of those who contributed to the document.
Section 7.0 References – provides a bibliography of sources cited throughout this TM.
Mendota Pool Bypass and Reach 2B Improvements Project 1-26 – October 2012 Project Description Technical Memorandum 2.0 Alternatives Formulation Process As part of implementation of the Settlement, Reclamation and DWR began the NEPA/CEQA process on the site-specific projects, including the Mendota Pool Bypass and Reach 2B Improvements Project, by initiating preparation of an EIS/R. An early step in producing the EIS/R is the formulation of the Final Alternatives that will be evaluated by the EIS/R. This chapter presents an overview of the development of the action alternatives. Attachment A – Alternatives Evaluation provides an in depth discussion and analysis of the key steps in the development and refinement of options and alternatives considered from the beginning of the Project
2.1 Alternatives Development Process Overview
Alternatives development progressed through several stages before being presented here in the Project Description TM. The process began with the Initial Options TM (SJRRP 2010d) which presented initial options for meeting Project goals and objectives. Input from Program Work Groups, stakeholders, and the public was collected. Subsequently, the initial options were refined based on impact evaluations, additional engineering analyses (appraisal level design), additional data collection, screening criteria, and public input to produce the Initial Alternatives.
Initial Alternatives were evaluated (Attachment A) using a set of evaluation and screening criteria developed pursuant to NEPA and CEQA requirements, and developed in coordination with Project proponents, to produce the range of reasonable alternatives presented here.
Using information obtained through evaluation and refinement, the final set of bypass, channel, and structure options were combined to create the Final Alternatives (Project/Action Alternatives), which are the basis for the Project EIS/R Project Description (see Section 3.0). The Project Alternatives provide a range of approaches to meet the Project purpose and need, which will allow for an assessment of environmental effects. The preferred alternative, to be identified in the Final EIS/R, may draw together components from multiple Project Alternatives.
Following development of the first draft of the Project Alternatives, Reclamation conducted a Value Planning Study to identify options to improve performance or reduce costs including phased implementation. The Value Planning Study team members included independent experts in the fields of engineering and cost estimating, geomorphology, biology, and restoration ecology, as well those familiar with the operational constraints in the Project area. The Study resulted in design proposals and comments provided to the Project team for review and possible inclusion in the Project.
Opportunities for stakeholder involvement were integrated throughout the alternatives formulation process. Figure 2-1 presents a graphical view of the process.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 2-1 – October 2012 San Joaquin River Restoration Program
Define Project Settlement and Purpose & Need, Develop Evaluation Information & Goals & Objectives Process Data from PEIS/R and Initial Studies Landowners and Landowners and Workgroups Input Workgroups Input
Refine Options Evaluate with & Finalize Develop Initial Screening Screening Options TM Criteria Criteria Project Description Landowners and Landowners and Data Workgroups Input Workgroups Input Collection & & Public Meeting Analytical Project EIS/R Tools
Figure 2-1 Alternatives Formulation Process
2.2 Stakeholder Involvement
The alternatives development provided the opportunity for early stakeholder involvement and input. Primary stakeholders include Federal, State, and local agencies, landowners, and the public. The following sections describe the level of involvement of the various stakeholder groups in the alternatives formulation.
2.2.1 Federal, State, & Local Agencies Federal and State Implementing Agencies involved in the SJRRP have representatives in the Technical Work Groups and Subgroups. These groups provide support for the development, evaluation, and refinement of concepts. The following groups had input during the alternatives formulation:
Fisheries Management Workgroup:
• DWR presented the initial options for the Reach 2B floodplain and Mendota Pool Bypass alignment at the November 10, 2009 meeting. • Refinement of initial options criteria and requirements related to fisheries were discussed during the December 11, 2009 Fisheries/Alternatives Subgroup. • The design flow for fish screening was discussed on February 3, 2010. • Further refinements to the floodplain and Mendota Pool bypass designs were presented and discussed on June 17, 2010, and passage requirements for non- salmonid native fish were also discussed.
Mendota Pool Bypass and Reach 2B Improvements Project 2-2 – October 2012 Project Description Technical Memorandum 2.0 Alternatives Formulation Process
• Passage at structures and passage design criteria were presented and discussed on August 19, 2010 and a recommendation was made to present to the Anadromous Fish Screen Program for feedback on fish screen designs. • A special subgroup was convened twice, on October 27, 2010 and February 24, 2011, with members of the workgroup and other agency staff with expertise in fish passage structure design to discuss technical and engineering issues related to the design of the fish passage structures. • A workshop was held on June 28, 2011 • Members of the workgroup participated in several calls with the Project team to discuss technical issues, approaches to resolving issues, and on-going analyses related to fisheries management. • The workgroup was involved in the review and comment of some Project-specific documents: the Initial Options TM, Analytical Tools TM, and this TM. • In addition, many calls and emails were exchanged with individuals in the workgroup to discuss specific issues. Environmental Compliance and Permitting Workgroup:
• The Reach 2B consultant presented the initial options for the Reach 2B floodplain and Mendota Pool Bypass alignment at the December 1, 2009 meeting. • The approach and use of analytical tools in the alternatives evaluation was presented and discussed at the meeting on May 18, 2010. • DWR presented the Reach 2B draft borrow areas investigation plan at the meeting on February 15, 2011. • The workgroup was involved in the review and comment of all Project-specific documents: the Initial Options TM, Environmental Data Needs TM, Analytical Tools TM, Environmental Survey Results TM, and this TM. • In addition, the Project team has regularly attended the workgroup’s meetings to provide Project updates and answer questions. Engineering and Design Workgroup:
• Engineering and Design Workgroup members developed pre-appraisal level structural options descriptions that addressed channel and floodplain conveyance given the site boundary conditions and a range of potential floodplain and channel characteristics. • Coordination with the workgroup has resulted in completion of an informal technical review by Reclamation’s Technical Service Center in Denver and initiation of a Value Planning Study organized by Reclamation. • In addition, the Project team has regularly attended the workgroup’s weekly conference calls to provide Project updates and answer questions.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 2-3 – October 2012 San Joaquin River Restoration Program
Water Management Workgroup:
• The Water Management Workgroup developed flow hydrographs for the purpose of evaluating site-specific alternatives under a range of potential flow schedules. Additionally, the group is coordinating with Reclamation and other stakeholders on Program operational guidelines. Members of all the workgroups were invited to a presentation on the alternatives evaluation to provide input on the mechanism for evaluating the alternatives at a meeting on February 18, 2011.
Fresno and Madera counties:
• Representatives from DWR spoke on the phone (July 27, 2010) and met with the Madera County Road Department (October 5, 2010) to describe the purpose of the Project and its effects on the San Mateo Avenue crossing and Drive 10 ½. DWR solicited input on the use and need for the crossing, as well as desired improvements. • A representative of DWR spoke on the phone with the Fresno County Road Maintenance Department on July 27, 2010 to describe the purpose of the Project and its effects on the San Mateo Avenue crossing. DWR solicited input on the use and need for the crossing, as well as desired improvements, but Fresno County did not desire to provide input because the crossing is not located within their right-of-way.
2.2.2 Landowners Meetings are held periodically with the landowners and representatives who have a stake in the Project or are located along the channel in the Project area to provide updates on Project status and collect input on alternatives development.
• The Reach 2B floodplain pre-appraisal level themes and Mendota Pool Bypass alignments were presented by DWR at the November 17, 2009 meeting. • Project status updates, overview of the publically available project-specific documents, concept refinement of the San Mateo Avenue crossing design and use of Little San Joaquin Slough, and the alternatives development process were presented and discussed, and comments were accepted at the May 27, 2010 meeting. • Project status updates, overview of new publically available project-specific documents, California State Lands Commission preliminary findings, and DWR’s land acquisitions process were presented and discussed, and comments were accepted at the March 24, 2011 meeting. • The California State Lands Commission draft administrative maps for Reach 2B, a brief Program update, and a Reach 2B Project update were presented at the October 3, 2011 meeting.
Mendota Pool Bypass and Reach 2B Improvements Project 2-4 – October 2012 Project Description Technical Memorandum 2.0 Alternatives Formulation Process
• The Project effects on Mendota Pool and other operations, details of Project components, and effects on infrastructure using large-scale maps were presented at the November 14, 2011 workshop. • Overview of borrow material needs and the status of geotechnical explorations was presented during the December 16, 2011 conference call. • Project overview, status, and a brief review of the alternatives were presented to stakeholders associated with Fresno Slough at the May 31, 2012 meeting. • In addition, many calls and emails were exchanged with individual landowners to discuss specific issues.
2.2.3 Public Reclamation and DWR held two public scoping meetings in July of 2009 for the purpose of initiating the NEPA and CEQA public input processes on the Project. During the scoping meetings and throughout the public comment period, Reclamation and DWR accepted comments on the proposed Project regarding the range of alternatives, the environmental effects, and the mitigation measures to be considered in the EIS/R. Suggestions regarding the pre-appraisal level themes were documented in the Scoping Report and have been considered in this TM.
The SJRRP also organized and held several public outreach meetings in the form of Technical Feedback Groups. The Project participated in the April 28, 2010, Restoration Goal Technical Feedback Group meeting by providing an overview and discussion of the Initial Options TM and Analytical Tools TM and in the May 17, 2012, Restoration Goal Technical Feedback Group meeting by providing a status update on the Project and an overview of technical challenges the team worked on during alternatives formulation.
When they are released for public review, the public would also have the opportunity to comment on the Draft and Final EIS/R documents prepared for the Project. Public meetings would be held following the publication of these documents and a public comment period would be observed.
2.3 Initial Options Formulation
The initial options were formulated based existing information and data, preliminary engineering analyses and screening, as well as input from Program Work Groups, stakeholders, and the public. Individual and group landowner meetings were held to present and obtain input on the initial options presented. One of the guiding Project objectives and subsequent analyses pertains to flow conveyance. A one-dimensional hydraulic model was completed during the development of initial channel/floodplain options to examine the largest range of practical and feasible floodplain widths given a reasonable range of management and habitat restoration strategies.
The following sources of information were utilized in the initial options formulation:
• Public scoping comments
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 2-5 – October 2012 San Joaquin River Restoration Program
• SJRRP documents • Pre-Settlement documents such as the San Joaquin River Restoration Study Background Document (McBain & Trush 2002) • NMFS and DFG guidance on the restoration of salmonid passage (NMFS 2001 and DFG 1998) • Preliminary pre-appraisal analyses prepared by DWR • Technical expertise of the Implementing Agencies Initial screening involved reviewing the options for consistency with the Settlement requirements and for technical feasibility. Any option deemed technically infeasible or beyond to the scope of the Settlement or contrary to its requirements were not carried forward for further consideration (see Section 4.0).
2.4 Alternatives Formulation
As part of implementation of the Settlement, Reclamation and DWR began the NEPA/CEQA process on the site-specific projects, including the Mendota Pool Bypass and Reach 2B Improvements Project, by initiating preparation of an EIS/R. An early step in developing the EIS/R is the formulation of the Final Alternatives that would be addressed by the document. The process diagram shown in Figure 2-2 depicts the steps in the formulation process.
Settlement Initial Options TM Improvements Project Goals Initial Refine Options Paragraphs into Initial and Objectives Options 11(a)(1) and Alternatives 11(a)(2)
Settlement Analytical Tools TM Restoration Goal Analyze and Water Evaluation Analytical Initial Management Criteria Tools Alternatives Goal with Tools
Evaluate Initial Alternatives with Criteria
Project Description TM
Project Final Description Alternatives
Figure 2-2 Alternatives Formulation Process Diagram
Mendota Pool Bypass and Reach 2B Improvements Project 2-6 – October 2012 Project Description Technical Memorandum 2.0 Alternatives Formulation Process
The initial guidance for developing the Project comes from language in the Settlement, specifically the Settlement’s goals and the Settlement defined improvements. The Settlement goals are:
The Restoration Goal (Settlement Paragraph 2):
… a goal of this Settlement is to restore and maintain fish populations in “good condition” in the main stem of the San Joaquin River below Friant Dam to the confluence of the Merced River, including naturally-reproducing and self-sustaining populations of salmon and other fish (the “Restoration Goal”).
The Water Management Goal (Settlement Paragraph 2):
…a goal of this Settlement is to reduce or avoid adverse water supply impacts to all of the Friant Division long-term contractors that may result from the Interim Flows and Restoration Flows provided for in this Settlement (the “Water Management Goal”).
The Mendota Pool Bypass and Reach 2B improvements defined in the Settlement are (Settlement Paragraph 11(a)):
(1) Creation of a bypass channel around Mendota Pool to ensure conveyance of at least 4,500 cfs from Reach 2B downstream to Reach 3. This improvement requires construction of a structure capable of directing flow down the bypass and allowing the Secretary to make deliveries of San Joaquin River water into Mendota Pool when necessary;
(2) Modifications in channel capacity (incorporating new floodplain and related riparian habitat) to ensure conveyance of at least 4,500 cfs in Reach 2B between the Chowchilla Bifurcation Structure and the new Mendota Pool bypass channel.
Alternatives formulation builds on the Settlement goals and project-specific improvements and progresses through three stages: initial options, Initial Alternatives, and Final Alternatives.
• Initial options represent the preliminary concepts and the basic components for project implementation. They were developed based on existing information and data, studies undertaken for the PEIS/R process, pre-appraisal level analyses and screening, as well as input from Program Work Groups, stakeholders, and the public. The initial options are described in the Initial Options TM (SJRRP 2010d). • The initial options were refined into Initial Alternatives based on additional concept refinement and engineering analyses, preliminary cost-benefit analyses, additional data collection, and input from the Program, Program Work Groups,
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 2-7 – October 2012 San Joaquin River Restoration Program
stakeholders, and the public. The Initial Alternatives represent a range of feasible implementation strategies incorporating appraisal-level design and analysis. • The Initial Alternatives were evaluated based on the evaluation criteria and with the tools described in the Analytical Tools TM (SJRRP 2010e). Attachment A documents the methods and results of the evaluation and makes recommendations for Final Alternatives to include in the main body of the Project Description TM (see Section 3.0).
2.5 Summary of the Alternatives Evaluation Process
A set of evaluation criteria were proposed in the Analytical Tools TM with which to evaluate the Initial Alternatives on the basis of flow conveyance and operations, fish habitat and passage, habitat restoration, geomorphology and sediment, groundwater, land use, economics, and socioeconomics, and costs. The criteria were developed based on the Project goals and objectives as a means of determining whether the Initial Alternatives meet those goals and objectives. During the appraisal-level design, additional detail was developed for each component and structure, new and refined modeling of the river channel and floodplains was conducted, and new data from field surveys became available. The criteria were further refined based on the available data, analyses, and the level of design, and the criteria were grouped into various factors, categories, and finally implementation feasibility, benefits, and impacts perspectives.3
Data representing the performance of the Initial Alternatives according to each applicable criterion was generated and input into an evaluation matrix spreadsheet. The evaluation process leveraged concurrent data collection efforts, engineering analyses and modeling, as well as stakeholder and public input. Using the evaluation matrix, the Initial Alternatives were scored according to their performance at the factor, category, perspective, and overall levels allowing for an understanding of the Initial Alternatives with respect to the goals and objectives of the Project. Detailed information on the evaluation process is provided in Attachment A.
2.5.1 Summary of the Evaluation Criteria Below is a summary of the evaluation criteria. The criteria are explained in-depth in Attachment A, Section 6.0.
Implementation/Technical Feasibility
Costs • Capital improvement costs: The costs associated with designing and building the Initial Alternative in total dollars.
3 Factors, categories, and perspectives are tiered groupings of the evaluation criteria. Factors are groupings of criteria, categories are groupings of factors, and perspectives are groupings of categories.
Mendota Pool Bypass and Reach 2B Improvements Project 2-8 – October 2012 Project Description Technical Memorandum 2.0 Alternatives Formulation Process
• Land costs: The estimated cost of land expected to be purchased for the Initial Alternative based on an average approximate value of $10,000 per acre. • Operation and maintenance costs: The annual dollars required to operate and maintain the Initial Alternative.
Time to Build • Time until action is functional: the number of months to construct and plant restoration vegetation for the Initial Alternative.
Objectives/Benefits Achievement
Fish Habitat and Passage • Rearing habitat: total acres of floodplain with a depth greater than 1.0 feet at 2,500 cfs • Shallow Water Habitat Quality: a rating based on the proportion of very shallow water habitat (less than 0.5 feet) to the amount of rearing habitat (greater than 1.0 feet) • Artificial structures in the migratory path: number of structures that adult salmon would need to pass. Each drop structure, dam sill, fish passage facility (or bifurcation structure), and crossing is considered as an individual structure. • Total number of steps at structures: the number of steps an adult salmon would need to jump or swim through. Each drop structure, dam sill, and fish passage facility step is considered as an individual step. • Fish screens along the migratory path: the number of fish screens with large diversion rates (greater than 100 cfs) that juvenile salmon may encounter along the migratory path. • Potential predation sites at structures: the number of potential predation sites that juvenile salmon may encounter along the migration path. Each drop structure, dam sill, fish passage facility (or bifurcation structure), fish screen outlet, and crossing is considered a potential predation site.
Habitat Restoration • Wetlands and other waters of the U.S. area: the acreage of restored habitat with hydrophytic vegetation and on hydric soils. • Sensitive vegetation alliance extent: the acreage of potential future sensitive vegetation alliances based on the Preliminary Planting Plans. • Wildlife habitat extent: the acreage of potential future wildlife habitat types resulting from the restoration. • Special status species habitat extent: the acreage of potential future habitat for special status wildlife species based on the wildlife habitat types.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 2-9 – October 2012 San Joaquin River Restoration Program
Geomorphology • Potential for lateral migration to impact levees: The estimated cost of providing erosion protection (revetment) on levees that may be impacted by lateral erosion.
Impacts
Groundwater • Acres of land in which groundwater levels rise above 5-foot monitoring threshold: The acreage of land outside the proposed levee alignments that is anticipated to have shallow groundwater elevations above the 5-foot monitoring threshold and is thus subject to mitigation measures to prevent waterlogging. • Acres of land in which groundwater levels rise above 7-foot monitoring threshold: The acreage of land outside the proposed levee alignments that is anticipated to have shallow groundwater elevations above the 7-foot monitoring threshold and is thus subject to mitigation measures to prevent waterlogging.
Land Use • Acres of farmland removed from production: The total acres of alfalfa, almond, grapes, other row crops (grouped), palm, and pistachio that would be permanently removed from production due to the construction and long-term operation of the Initial Alternatives.
Socioeconomics and Economics • Reduction in annual agricultural production values: The total production value based on unit production values and the acreage permanently removed from production due to the construction and long-term operation of the Initial Alternatives.
Environmental • Wetland impacts: The estimated acreage of direct impacts to wetlands resulting from the Initial Alternatives. • Sensitive vegetation alliance direct impacts: The estimated acreage of direct impacts to sensitive vegetation alliances resulting from the Initial Alternatives. • Special status wildlife habitat impacts: The estimated acreage of direct impacts to special status wildlife habitat resulting from the Initial Alternatives. • Historic properties potentially effected: The number of recorded historic properties identified within the extents of the Initial Alternatives. • Buried deposits sensitivity: The highest buried deposits sensitivity within the extents of the Initial Alternatives based on the landform age scale.
2.5.2 Scoring Alternatives Data and Professional Judgment Most of the data presented use objective measurements for each criterion, such as acres, dollars, or miles, based on appraisal-level designs for each alternative. Some of the criteria in the evaluation use qualitative assessments and rely on professional judgment to estimate results. Assumptions about current conditions and future effects of the
Mendota Pool Bypass and Reach 2B Improvements Project 2-10 – October 2012 Project Description Technical Memorandum 2.0 Alternatives Formulation Process alternatives are inherently involved at the current level of design. These assumptions have been based on information collected from similar projects and professional experience.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 2-11 – October 2012 San Joaquin River Restoration Program
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Mendota Pool Bypass and Reach 2B Improvements Project 2-12 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.0 Description of Alternatives This chapter describes the Final Alternatives developed for the Project. Each of the Final Alternatives consist of a Floodplain Initial Alternative and a Bypass Initial Alternative as described in Attachment A. Final Alternatives are considered to comply with the terms of the Settlement, substantially meet the Project goals and objectives, and have benefits potentially offsetting their impacts. Final Alternatives will be assessed for environmental impacts to the various resource areas in the Project EIS/R and hereafter are called Alternatives. The preferred alternative, to be identified in the Final EIS/R, may draw together components from multiple Project Alternatives.
3.1 Alternatives Development
3.1.1 NEPA Requirements This development of alternatives is being prepared by Reclamation as the Project proponent and Federal lead agency under NEPA. For the alternatives including the proposed action, NEPA requires that Federal government agencies shall (Sec. 1502.14):
(a) Rigorously explore and objectively evaluate all reasonable alternatives, and for alternatives which were eliminated from detailed study, briefly discuss the reasons for their having been eliminated.
(b) Devote substantial treatment to each alternative considered in detail including the proposed action so that reviewers may evaluate their comparative merits.
(c) Include reasonable alternatives not within the jurisdiction of the lead agency.
(d) Include the alternative of no action.
(e) Identify the agency's preferred alternative or alternatives, if one or more exists, in the draft statement and identify such alternative in the final statement unless another law prohibits the expression of such a preference.
(f) Include appropriate mitigation measures not already included in the proposed action or alternatives.
3.1.2 CEQA Requirements This development of alternatives is being prepared by DWR as the Project proponent and State lead agency under CEQA. Section 15126.6 of the CEQA Guidelines requires that an EIR, "describe a range of reasonable alternatives to the project, or to the location of the project, which would feasibly attain most of the basic objectives of the project, but would avoid or substantially lessen any of the significant effects of the project, and evaluate the comparative merits of the alternatives."
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-1 – October 2012 San Joaquin River Restoration Program
Additionally, Section 15126.6 of the Guidelines states:
• The specific alternative of "no project" shall also be evaluated along with its impact. • An EIR need not consider every conceivable alternative to a project. Rather, it must consider a reasonable range of potentially feasible alternatives that will foster informed decision making and public participation. An EIR is not required to consider alternatives which are infeasible. . . . The range of potential alternatives to the proposed project shall include those that could feasibly accomplish most of the basic objectives of the project and could avoid or substantially lessen one or more of the significant effects. • The EIR should briefly discuss the rationale for selecting the alternatives to be discussed. The EIR should also identify any alternatives that were considered by the lead agency but were rejected as infeasible during the scoping process and briefly explain the reasons underlying the lead agency’s determination…Among the factors that may be used to eliminate alternatives from detailed consideration in an EIR are: (i) Failure to meet most of the basic project objectives,
(ii) Infeasibility, or
(iii) Inability to avoid significant environmental impacts.
Since this is a joint Federal-State Project, the EIS/R is being prepared compatibly with NEPA. To that end, the Alternatives are to be analyzed on an equal, non-preferential basis and at an equal level of detail (consistent with NEPA standards). The proposed project/preferred alternative will be identified in the Final EIR, with that selection to be informed through the CEQA process.
3.2 Overview of Alternatives
The Project Description TM presents a No-Action/No-Project and four action alternatives to implement the Project. Each action alternative includes the actions called for in the Settlement for the Mendota Pool Bypass and Reach 2B. Under the No-Action/No-Project alternative, the Project would not be implemented. Of the four action alternatives, there are two methods of bypassing Restoration Flows around Mendota Pool, two floodplain widths, and four ways to divert water into Mendota Pool.
Project alternatives include the following:
• No-Action/No-Project Alternative • Compact Bypass with Narrow Floodplain and South Canal • Compact Bypass with Wide Floodplain and Bifurcation Structure
Mendota Pool Bypass and Reach 2B Improvements Project 3-2 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
• Fresno Slough Dam with Narrow Floodplain and Short Canal • Fresno Slough Dam with Wide Floodplain and North Canal
3.3 No-Action/No-Project Alternative
The No-Action/No-Project Alternative4 is required for the analysis of environmental effects under NEPA (the No-Action Alternative) and CEQA (the No-Project Alternative). Under this alternative, the Project would not be implemented. The No-Action Alternative is not consistent with the Settlement.
Existing conditions for the No-Project Alternative will be developed for each resource area based on the availability of historical data and recent observations.
Future conditions for the No-Action Alternative will be based on reasonably foreseeable actions that would occur without the Project, including projects that are currently authorized, funded, permitted, or highly likely to be implemented. The planning period for the future condition evaluation would vary depending on the resource area. The conditions under the No-Action Alternative are the conditions that are predicted to exist in the Project area during the planning period if the Project is not implemented
No-Action Conditions If the Project were not implemented, the components described in the Alternatives would not be implemented; however, other components of the SJRRP would be implemented if they have completed appropriate environmental reviews and have been approved. Likely future conditions include the SJRRP components analyzed in the PEIS/R for the SJRRP, the Interim Flows analyzed in the Interim Flow Environmental Assessment (Reclamation 2010), and other reasonably foreseeable actions expected to occur in the Project study area. It is assumed for the No-Action condition that agriculture would continue and cropland would be the dominant cover type, consistent with the existing condition.
The No-Action Alternative generally assumes no channel or structural improvements would be made in Reach 2B, and Restoration Flows would be reduced to not exceed the existing Reach 2B capacity or rerouted/partially rerouted around Reach 2B. The following assumptions about No-Action will be evaluated in the resource sections of the Project EIS/R.
Fisheries In the No-Action Alternative, the maximum channel conveyance would be limited to the existing capacity (approximately 810 cfs in Reach 2B, SJRRP 2011 – Appendix I: Underseepage Analysis). Fish passage improvements would not be provided at structures
4 The No-Action Alternative was originally described in the Initial Options TM (SJRRP 2010d).
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-3 – October 2012 San Joaquin River Restoration Program
(Chowchilla Bifurcation Structure, San Mateo Avenue, and Mendota Dam). However, the remainder of the SJRRP would proceed, and salmon would be reintroduced into the San Joaquin River. Each spring during their outmigration, downstream migrating juveniles would be entrained in diversions from Mendota Pool and succumb to high rates of predation by non-native fish present in Mendota Pool. Adult salmon would be blocked on their upstream migration at Mendota Dam in all years except wet year types. Blocked adult salmon would be exposed to poaching in the river below Mendota Dam and poor water quality later in the year. There is no spawning substrate in Reach 3, downstream of the dam, so blocked adult fish would require alternative efforts to reach spawning grounds or would not spawn successfully.
Habitat Under the No-Action Alternative, habitat conditions in the Project area may change to the extent that Interim and Restoration flows may recruit new vegetation in some areas. In this alternative, if Restoration Flows were to enter Reach 2B, the condition of the narrow strips of native riparian vegetation along the channel banks downstream of the San Mateo Avenue crossing would be maintained by the relatively stable water level held by Mendota Dam. Upstream of San Mateo Avenue, riparian vegetation may recruit along the wetted channel banks unless vegetation removal is employed.
Seepage The No-Action Alternative would maintain the existing levee alignments and heights and maximum conveyance would continue to be limited to the existing capacity (approximately 810 cfs, SJRRP 2011 – Appendix I: Underseepage Analysis). If Restoration Flows enter the existing Reach 2B, there would probably be a minimal increase in seepage from the river channel but since capacity would remain unchanged, this may be similar to the seepage experienced during Interim Flows under existing conditions.
Land Use, Agriculture, Economics & Socioeconomics Under No-Action conditions, future land use in the area is unlikely to change. Reach 2B is in the unincorporated areas of both Fresno and Madera Counties. The nearest incorporated cities are Firebaugh and Mendota, both in Fresno County. Population is expected to increase annually, compounded, by 1.8 percent and 2.5 percent in Fresno and Madera Counties, respectively, between 2000 and 2050 (CDF 2007). Most of that growth would likely occur in areas near the main cities in each of the counties. While population and economic projection data for specific unincorporated subareas of the counties are unavailable, neither agricultural nor non-agricultural activity is likely to expand substantially in the Mendota area.
If the Reach 2B Project is not implemented, future socioeconomic conditions in the pertinent Fresno and Madera County areas relative to conditions in other areas in the two counties would be expected to be similar. It is expected that the Reach 2B area would remain in agriculture and that most of the working population in the area would remain employed in agriculture and related industries.
Mendota Pool Bypass and Reach 2B Improvements Project 3-4 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Geomorphology The No-Action Alternative would maintain the existing levee alignments and heights and maximum conveyance would continue to be limited to the existing capacity (approximately 810 cfs). If Restoration Flows enter the existing Reach 2B sand transport would likely increase; however, recent sediment continuity studies have predicted that sand inputs from Reach 2A under Restoration Flows will likely result in net deposition in the upper segment of Reach 2B and potentially down to the Mendota Pool. The No- Action Alternative would not likely change the existing geomorphic conditions in Reach 2B.
3.4 Elements Common to All Action Alternatives
All Alternatives would be designed to provide:
• Conveyance of at least 4,500 cfs in Reach 2B and the Mendota Pool Bypass channel • Diversion and screening of up to 2,500 cfs from Reach 2B into Mendota Pool Additionally, some constructed elements are also common to all Alternatives. Those elements are described below.
3.4.1 Fish Habitat and Passage The amounts of fish habitat and the number of structures fish would need to pass vary among the Alternatives; however, some conditions and criteria are consistent across Alternatives and warrant discussion here.
One of the primary focuses of Alternatives is to provide floodplain and riparian habitat to provide benefit to migrating juvenile and adult salmonids and other native fishes. Floodplain and riparian habitats in the Alternatives would include a variety of native plant communities suited to the hydrology, soils, and climate of Reach 2B and the San Joaquin Valley (see additional discussion below under Habitat Restoration).
The Alternatives also include provision of fish passage at structures for salmonids and other native fish. These structures vary by alternative but overall include a culverted crossing at San Mateo Avenue, fish screens, fish passage facilities, grade control structures, bifurcation structures (under certain flows), and Mendota Dam. The designs for structures with fish passage components would be based on criteria in Anadromous Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage at Stream Crossings (NMFS 2001). Specifically, the alternatives would provide suitable hydraulic conditions for passage of up-migrating adult and juvenile salmonids, out- migrating juvenile salmonids, and inter-reach migration of other native fish between Reach 2A and Reach 3. Suitable hydraulic conditions include those conditions which the species is physically capable of passing and do not cause undue stress on the animal. The passage features would be designed to cause no physical harm to fish. The design criteria are structured around the life stages of the target anadromous species and the timing of the runs for upstream movement of adult fall and spring run Chinook and winter
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-5 – October 2012 San Joaquin River Restoration Program
steelhead and the upstream and downstream movement of juvenile life stages spawned from these runs. Recommended criteria are based on a combination of swimming ability of the fish species as reported in scientific papers and criteria in agency design guidelines. Recommended design criteria to provide for successful fish passage (depth of flow, suitable velocity ranges and jump height) are provided in Table 3-1. The design criteria for a particular species would be met over the associated flow range (minimum flow to maximum flow).
All the Action Alternatives include facilities that fish would encounter or need to pass to migrate between the bypass and Reach 2A (from downstream to upstream). The Lone Willow Slough fish screen (see Section 3.4.8) is included in all alternatives, and each alternative includes other facilities specific to the alternative. Each structure represents a potential stressor for adult salmon and potential predation site for juvenile salmon. However, each structure would be designed to perform according to the fish passage design criteria. In addition, the channel and floodplain incorporate riparian plantings to provide cover, woody material, and velocity variability, while the design footprint allows sufficient space to accommodate channel structure variability, all of which may help to reduce stress and predation.
During construction, impacts to fish would be minimized by including some or all of the following measures:
• Temporary bypass facilities around construction areas that meet fish passage criteria • Construction in the dry • Phased construction that would allow passage to continue in the channel or in the completed portions of structures while other portions are built • Fish rescue and relocation
Mendota Pool Bypass and Reach 2B Improvements Project 3-6 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-1 Fish Passage Design Criteria
3
1
2
stage - Depth Depth Species Velocity Migration Migration Maximum Maximum Life Frequency Timeframe Height Jump Minimum Pool Pool Minimum Minimum Flow Minimum Maximum Flow Minimum Water
years cfs cfs fps feet feet feet
Spring and All years 4 5 Adult 115 4,500 4.0 1.2 1.0 fall pulse except CL Late spring Chinook Juvenile All years 6 5 diminishing 125 n/a 1.0 1.0 0.5 salmon (upstream) except CL flows
Juvenile All years 7 5 Nov-May 85 n/a n/a 1.0 n/a (downstream) except CL
Spring and All years 4 5 Adult 115 4,500 4.0 1.2 1.0 fall pulse except CL Late spring Juvenile All years 6 5 Steelhead diminishing 125 n/a 1.0 1.0 0.5 (upstream) except CL flows
Juvenile All years 7 5 Nov-May 85 n/a n/a 1.0 n/a (downstream) except CL None – Spring W and NW 8 Sturgeon Adult 1,138 4,500 6.6 3.3 swim n/a pulse years through
Spring All years 6 9 9 9 Lamprey Adult 125 4,500 n/a pulse except CL W, NW, None – Other Spring 10 Adult and ND 543 4,500 2.5 1.0 swim n/a native fish pulse years through W = wet; NW = normal wet; ND = normal dry; CL = critical low 1 Recommended velocities are for drop structures or structures with short longitudinal lengths. For structures with longer lengths (e.g., culverts and bifurcation structures under certain conditions), maximum velocities would be based on Anadromous Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage at Stream Crossings (NMFS 2001). 2 Minimum water depth criteria based on 1.5 times body depth or 1 feet depth, whichever is greater. 3 Maximum jump height criteria based on criteria in Anadromous Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage at Stream Crossings (NMFS 2001). 4 Based on Exhibit B lowest flow in the fall spawning period (starts Oct 1) for the desired frequency; all Spring Pulse Flows are higher. 5 Pool depths to be based on criteria in Anadromous Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage at Stream Crossings (NMFS 2001). 6 Based on lowest flow within Exhibit B Spring Pulse Flow period for the desired frequency. 7 Based on lowest flow within desired migration period for the desired frequency. 8 Wet and normal wet years constitute 50% of years in the historical record. Based on an analysis of varying Restoration Flows management strategies (Reclamation 2010); flows with a 50% exceedance could range from 1,138 to 4,500 cfs. 9 Lamprey designs to be based on criteria in Best Management Practices for Pacific Lamprey (USFWS 2010) 10 Wet, normal wet, and normal dry years constitute 80% of years in the historical record. Based on an analysis of varying Restoration Flows management strategies (Reclamation 2010); flows with an 80% exceedance could range from 543 to 4,500 cfs.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-7 – October 2012 San Joaquin River Restoration Program
3.4.2 Levees The location, length, and height of the levees vary among the Alternatives; however, some design criteria and features would be consistent across all Alternatives and warrant discussion here.
Levees would be required along the Project area to contain Restoration Flows. While the height and footprint of the levees vary according to their location along the channel and the ground elevation, the capacity, freeboard, and cross-section would be consistent. Levees would be designed to maintain 3 feet of freeboard on the levees at 4,500 cfs. Levee design would be based on the USACE Engineer Manual 1110-2-1913-Design and Construction of Levees guidelines (USACE 2000a) and Engineer Manual 1110-2-301 Guidelines for Landscape Planting and Vegetation Management at Floodwalls, Levees, & Embankment Dams (USACE 2000b). The design includes seepage control measures, inspection trenches, maintenances roads, and drainage trenches to direct off-site drainage.
Levee alignments maintain a 300-foot buffer zone, where appropriate, between the levee and river channel to avoid impact to levees over time due to potential channel migration. In areas where a minimum 300-foot buffer zone between the main river channel and levee cannot be maintained, bank revetment would be incorporated in the design.
The levees would be designed to have sideslopes of 3 horizontal to 1 vertical (3H to 1V) on the waterside and landside. A maintenance road and surface drainage ditch would also be included. Surface drainage ditches would only be intended to capture and direct runoff; they are not intended to address groundwater seepage or through-levee seepage. Due to historical seepage and lack of geotechnical data, it was assumed for cost purposes that all of both new levees adjacent to potentially impacted lands (approximately 90 percent of the total levee length) would contain slurry walls5. By following the USACE standards, all levees would have an inspection trench. Additional data collection and analysis would be required to verify the groundwater conductivity rates of the in situ and borrow soils and to finalize the design of seepage control measures.
The levee alignments shown on the plan views of the alternatives may be adjusted during final design. Adjustments may be made for several reasons including to improve flow conditions on the floodplain, to improve habitat conditions on the floodplain, to reduce potential erosion, to accommodate adverse soil conditions, and to avoid existing infrastructure among others. The final levee alignments will be within the impact areas evaluated in this document.
5 A slurry wall is a building technique to reinforce areas of soft earth that is near open water or a high groundwater table. The wall is constructed to act as a barrier to prevent water from flowing through it. Typical construction is to dig a trench to create a form for each wall, then the trench is filled with cement slurry, reinforcement is added to the trench (like rebar), then the trench is filled with concrete which displaces the slurry.
Mendota Pool Bypass and Reach 2B Improvements Project 3-8 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.4.3 Seepage Control Measures Seepage of river water through or under levees is a concern for levee integrity and adjacent land uses. Through-seepage, water that seeps laterally through the levee section, would be addressed through proper levee design and construction (e.g., selection of low porosity materials and proper compaction). Under-seepage, water that seeps laterally by travelling under the levee section, is primarily controlled by the native soils beneath the levee and seepage control measures would be included where native soils do not provide sufficient control. Seepage control measures would be included, as necessary, in the Project in areas where under-seepage is likely to affect adjacent land uses. Seepage control measures could include: slurry walls, tile drains, seepage wells, seepage berms, land acquisition (fee title or seepage easements) and other measures that can be implemented within the Project area.6 While slurry walls were assumed for cost purposes, any of these control measures could be implemented.
3.4.4 Borrow Borrow material would primarily be required for the construction of the levees, but it may also be utilized in the construction of other structures for foundation or backfill material. Levees may be constructed entirely of local borrow material, a mix of local and imported borrow material, or just imported borrow material. Borrow locations will be determined after a geotechnical exploration of the local borrow areas is complete; the exploration will determine the suitability of local soils for use as borrow material. Until the exploration can be complete, it is assumed that all levee fill will come from local borrow sites. Investigation and analysis of potential borrow sites is ongoing by DWR, and the borrow area information will be updated as new information becomes available. Topsoil from local borrow areas would be stockpiled for reuse at the borrow site or within the Project Area.
The locations of borrow areas are dependent on the locations of suitable materials. To the extent that suitable materials and the locations for floodplain grading coincide, borrow from those areas may be preferred. Borrow from within the Project Area will be designed to be compatible with native fish habitat and uses by either reconnecting to the river channel or by restoring to an appropriate elevation to prevent stranding.
It is estimated that up to 350 acres of land total will be needed for borrow areas. This includes borrow locations inside and outside the Project levees (identified as Potential Borrow Area on Figure 1-2). Borrow areas will avoid natural areas to the extent practicable.
6 Tile drains are buried perforated pipes which intercept groundwater and redirect it to a discharge point. Because the drains have lower resistance to flow, the groundwater table can be kept artificially low in areas near the pipe. Seepage wells are groundwater wells that are used to pump and draw down the water table where seepage is occurring. Seepage berms are berms placed on the landside of a levee to add additional weight and width to the levee to counteract seepage.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-9 – October 2012 San Joaquin River Restoration Program
3.4.5 Levee protection Each Alternative generally provides a minimum 300-foot buffer between the existing channel and the proposed levee, where appropriate and feasible. For locations where the 300-foot buffer was not included, erosion protection for the levee in the form of revetment would be included. The revetment would be riprap material covered by soil and then planted to provide a vegetated surface. However, softer approaches, such as bioengineering or dense planting, may be considered during design depending on velocities and scour potential. Locations that require revetment include areas where the 300-foot buffer was not included due to the proximity of existing infrastructure, near the proposed structures, and along river bends less than 300 feet from the levee.
3.4.6 Removal of existing levees Removal of portions of the existing levees is included and designed to expand the inundation area of the floodplain out to the proposed levees and improve connectivity between the river channel and proposed floodplain. The locations of existing levee removal are based upon the hydraulic performance of the channel and floodplain. In certain locations, however, highly desirable existing vegetation (native and sensitive vegetation communities that can serve as seed banks for future vegetation communities) can be found on the existing levees. Where hydraulic performance and connectivity of the floodplain would not be negatively affected, portions of the existing levees with highly desirable vegetation would remain in place.
3.4.7 Floodplain Grading Floodplain grading would be included with all of the Alternatives. Floodplain grading would not involve wholesale recontouring of the entire floodplain, but would include any or all of the following at locations to be determined during design:
• Creating high-flow channels through the floodplain to increase the inundation extent at lower flows • Connecting low-lying areas on the floodplain to the river to prevent stranding • Removing high areas where flow connectivity would be impeded (e.g., farm road grades) • Excavating floodplain benches adjacent to the river channel to increase the frequency of inundation • Creating greater inundation depth diversity on the floodplain Floodplain grading can provide benefits to salmon and other native fish by allowing inundation to occur at lower flows, by distributing suitable rearing habitats further into the floodplain, by connecting rearing habitat to primary production areas (shallow water habitat), and by providing escape routes during receding flows.
The Figure 3-1 provides an example of how various floodplain grading approaches can be used to expand inundation on the floodplain. The Existing Channel graphic shows an example of how inundation would occur without floodplain grading. The Lowered Floodplain example shows how floodplain benches, lowered areas to either side of the channel, could be used to inundate floodplain areas at lesser flows. This graphic also
Mendota Pool Bypass and Reach 2B Improvements Project 3-10 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives shows how lowered floodplains could affect inundation at moderate flows. The High Flow Channels graphic shows an example of how high flow channels, side channels that initiate at larger flows than the main channel, could be used to expand floodplain inundation.
3.4.8 Lone Willow Slough Fish Screen Lone Willow Slough connects to the river at approximately RM 215.9 just downstream of the Chowchilla Bifurcation Structure. All Alternatives include construction of a fish screen at this diversion. During flood control releases from Friant Dam and when the Exchange Contractors are exercising their water rights on the San Joaquin River, in lieu of taking substitute water from the Delta Mendota Canal, up to 125 cfs of water may be diverted for irrigation from Reach 2B into the Lone Willow Slough. A screen would be necessary to prevent fish from entering the canal when flows are being diverted. The fish screen structure consists of a 15-foot by 21-foot concrete hollow box, with the river side of the box open to river flows and the back of the box fitted with a board guide to control diversion into the irrigation canal. The opening at the riverside includes an automated cleaner system, trash rack and a fish screen to prevent migrating fish from entering the intake. The screen would be designed to meet NMFS 2008 criteria.
3.4.9 Infrastructure for Fish Monitoring The designs for control structures, fish passage facilities, and fish screens include security fences and gates, mounting hardware, and electrical supply in order to conduct fish monitoring activities. The fish monitoring activities themselves are not included in this Project.
3.4.10 Existing infrastructure relocations or floodproofing Existing infrastructure (see Figure 3-2) such as groundwater wells, pumps, electrical and gas distribution lines, water pipelines, and canals are located in the Project area and would require relocation, retrofitting, or floodproofing to protect them from future Restoration Flows and increased floodplain area. The cost to perform the relocations, retrofits, and floodproofing would be included in the Project cost; the actual relocation, retrofit, or floodproofing work may be performed by others. As a result of the Project, some existing infrastructure may be unnecessary in the future (e.g., power lines that service pumps relocated to outside the project area). In these cases, infrastructure may be demolished or abandoned in place.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-11 – October 2012 San Joaquin River Restoration Program
Figure 3-1 Example Floodplain Grading Approaches
Mendota Pool Bypass and Reach 2B Improvements Project 3-12 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Figure 3-2 Existing Infrastructure in the Project Area
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-13 – October 2012 San Joaquin River Restoration Program
Electrical and Gas Distribution The length of electrical and gas distribution line impacted by each Alternative was identified for possible relocation. Information from PG&E was available for portions of the area in shapefile format and was supplemented by field data. At the current level of design, it was assumed that the length of existing electrical and gas distribution line found within the Project area would need to be replaced. It is anticipated that some service could be discontinued in the future; the extent of discontinued and replaced service will be refined during the design phase.
Canals and Drains The length of canals impacted by each Alternative was identified for possible relocation. On-farm canals and drains visible on the LiDAR imagery (Central Valley Floodplain Evaluation and Delineation (CVFED) 2009) and identified during on-site field meetings with landowners were quantified. At the current level of design, it is unknown how canals and drains outside the Project area would be reworked as a result of the impacted canals and drains. It is anticipated that some portions of canals and drains could be discontinued in the future; the extent of discontinued and replaced canals will be refined during the design phase. No subsurface drains were able to be quantified; however, some are believed to exist within the area.
Lift Pumps The number of lift pumps impacted by each Alternative was identified for possible relocation. Lift pumps visible on the LiDAR imagery (CVFED 2009) or noted in the Calfish database (Pacific States Marine Fisheries Commission 2007) were assumed to require relocation to new facilities on the edge of the proposed levees. A pilot channel dug from the low flow river channel to the intake of the relocated pumps was also assumed. Locations in the Calfish database were confirmed using the LiDAR imagery when possible.
Groundwater Wells The number of existing wells impacted by each Alternative was identified for possible floodproofing or relocation. Wells were identified within the area using aerial photography. It is recommended that the DWR wells database be consulted for an estimate of abandoned wells that have not been destroyed, so that these old wells would not be conduits for flood waters to the groundwater. A formal well canvas is recommended. Floodproofed wells would be provided with year-round vehicular access via a raised roadbed across the floodplain. The roadbed could include multiple culverts to support floodplain connectivity, depending on the length of the access road and its effect on floodplain flows.
Regulating Reservoirs The number of irrigation regulating reservoirs was identified for possible relocation. Reservoirs were assumed to be a typical size, contain one lift pump, and half of the reservoir located below the surrounding grade and half above the surrounding grade.
Mendota Pool Bypass and Reach 2B Improvements Project 3-14 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Other Utilities Other infrastructure was identified within the impacted areas. Other facilities include: high voltage transmission lines, gas lines, and water pipelines. High voltage transmission lines are assumed to be high enough to not be impacted. Gas lines are typically attached to bridges or buried below the river when crossing the river and were assumed not to require relocation. Water pipelines were quantified from existing maps and discussions with landowners. Water pipelines may be relocated or abandoned depending on their future use requirements. Mitigation would be required when crossing a service line (e.g., gas, water, electrical) with a levee depending on the depth of cover.
3.4.11 Construction Access Access for vehicles carrying materials, equipment, and personnel to and from the construction area would be provided via several existing roadways in the Project vicinity (see Figure 3-3). Improvements may be required to upgrade roadways, pavements, and crossings for anticipated construction traffic and loads, provide adequate turning radii and site distances, and to control dust on non-paved roads. Anticipated improvements include:
• Eastside Drive – Approximately 0.6 miles of dirt road starting at Road 10 ½ will likely require overlaying, and the implementation of dust control measures. Measures could include the use of water trucks or dust palliative for dust control or gravel placement where necessary. • Chowchilla Canal Road/Road 13 – Approximately 0.3 miles of road starting at Eastside Drive will likely require some overlaying and the implementation of dust control measures. Measures could include the use of water trucks or dust palliative for dust control or gravel placement where necessary. • San Mateo Avenue – Approximately 0. 5 mile of gravel and 1.5 miles of oil-dirt road starting at the existing San Joaquin River levees will likely require some overlying and the implementation of dust control measures. Measures could include the use of water trucks or dust palliative for dust control or gravel placement where necessary. • Bass Avenue Canal Crossings – These crossings may need additional bracing and shoring to ensure that they will be able to support the load of the construction equipment and activities. All the construction equipment on Bass Avenue will be within the legal loads (see note below). This crossing is on the Fresno County replacement list. • Delta Mendota Canal Crossing – This crossing may need additional bracing and supports to ensure that it will be able to support the load of the construction equipment activities. The above assumes that legal loads would be used on all roads, and once construction is completed, the roads would be returned to the same condition as they were prior to the Project.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-15 – October 2012 San Joaquin River Restoration Program
Figure 3-3 Construction Access Routes
Mendota Pool Bypass and Reach 2B Improvements Project 3-16 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.4.12 Operations and Maintenance The Project includes long-term operations and maintenance of the proposed facilities and features.
Maintenance Levees will require maintenance for vegetation management, access roads, levee inspections, levee restoration, rodent control, minor structures, encroachment removal, levee patrolling during flood events, and equipment costs. Levee vegetation management includes equipment to drag the levee banks or aquatic-safe herbicide applications. Maintenance of access roads includes replacing gravel or scraping and filling of ruts to keep the roads in good condition. Levee restoration includes restoring areas with erosion or settlement problems or adding armor. Rodent control includes setting traps with bait and periodically checking the traps. Minor structures maintenance includes repair or replacement of gates, locks or fences. Encroachment removal involves removing illegally dumped materials.
Floodplain maintenance includes vegetation management for invasives, periodic floodplain and channel shaping to retain capacity and prevent fish stranding, and other floodplain maintenance activities such as debris removal.
San Mateo Avenue maintenance includes maintenance when flows overtop the road and annual maintenance to keep the crossing functional and ensure that it can meet fish passage requirements, these include cleaning the culverts of debris or sediment, clearing any debris from the roadway prior to opening after flows have receded, and repairing or replacing minor structures. Minor structures maintenance includes replacing gate locks, painting gates, replacing lost or damaged signage, and lubing gates.
Control structures and Fresno Slough Dam maintenance includes annual operating maintenance for control gates, lubing the fittings, greasing and inspecting the motors, replacing parts and equipment, and cleaning the trash rack. Work needed for the radial gates includes inspection of gates and seals and periodic replacement of seals. Work needed for the trash rake includes periodic repair or replacement of components, inspecting for operation, and greasing and inspecting the motors.
Fish screen maintenance is needed to ensure that the screen is functioning to NMFS standards at all times and capable of diverting the required flow. Fish screens maintenance includes removing the screens for cleaning, replacing screens when needed, periodic repair or replacement of brush cleaning system components, periodic repair or replacement of trash rake components, inspection for operation, greasing and inspecting motors.
Fish screen maintenance is needed to ensure that the barrier is functioning to NMFS standards at all times and capable of passing the required flow. Fish barrier maintenance includes periodic repair or replacement of screens and debris removal.
Fish screen maintenance is needed to ensure that the barrier is functioning to NMFS standards at all times. Fish passage facility maintenance includes removing sediment and
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-17 – October 2012 San Joaquin River Restoration Program
debris from the facility, inspection of gates and seals and periodic replacement of seals, periodic repair or replacement of weir gates, periodic repair or replacement of supplementary water system components, inspection for operation, greasing and inspecting motors.
Water diversion canal maintenance includes sediment removal and channel re-shaping.
Mendota Dam maintenance includes periodic minor upstream sediment removal in order to operate the Short Canal only.
Maintenance Schedule All maintenance activities, when possible, would be timed to minimize the impacts to fish. All activities would require environmental clearance to be completed prior to any annual maintenance or repairs that are not deemed an emergency. Access and safety concerns are the main driver for timing of the maintenance activities, but can be scheduled around fish migration. Ultimately, the schedule may be impacted by compliance with the clearance to conduct the work and timing of flows.
Maintenance of levees and floodplains for aquatic-safe herbicide treatment would occur sometime between spring and fall and would depend on the plant species that are being treated. Typically the herbicide would be administered prior to the plant going to seed and may need to be sprayed more than once. Disking for vegetation management usually occurs twice within the year; once in early spring after the rainfall season and then again in late summer prior to plants going to seed. Access road and levee restoration work would likely be done in the summer after the rainfall season, and timing and projects would be dependent on environmental clearance for small mammals, nesting birds or burrowing owls, and other wildlife species. Rodent control would likely be done by a pest control advisor and would likely be done in the spring through fall and not during the rainfall season. All levee and floodplain work can be impacted by the presence of nesting birds, so in some areas work may not begin until mid-summer (after June).
Timing of the maintenance of structures within the waterways would depend on the flow hydrograph and forecasted flows, but can typically be expected in the summer/fall after high spring flows have receded. Cleaning of the in-channel structures would typically occur when flows are low enough to allow crews and equipment to enter the river safely to access the structures. San Mateo Avenue may be cleared or repaired earlier for access as soon as flows recede and are not likely to increase for the remainder of the water year. If earlier, this work would only be for road access and would not be located in the channel itself.
Debris that collects on trash racks, screens, ladders, or other fish passage structures will need to be periodically removed but will likely be scheduled based on the operation permits for these structures. Annual maintenance cleaning would be expected after the fish migration, but will need to be timed when flows have receded.
Lubing and annual gate maintenance would likely be in the late summer or early fall prior to winter and spring flows to make sure the structures are operating properly and to
Mendota Pool Bypass and Reach 2B Improvements Project 3-18 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
provide time for repairs and ordering parts if needed. This will likely begin after the annual State budget is adopted and ordering of parts would be allowed.
For the Short Canal Option, the boards would be placed back into Mendota Dam. This could occur at any time, but would likely occur during the irrigation season. The fish passage structure at the dam would allow for fish passage when the boards are in-place.
Water diversion canals that require maintenance could be isolated from the river system by closing the headgates at the canals which will not impact fish migration.
Operations There are no operations for levees or floodplains.
San Mateo Avenue operations include closing the gates to the crossing during high flows and reopening once flows have receded.
Control structures and Fresno Slough Dam operations include operating the motors for the control gates, inspecting and assessing the gates, adjusting the gates for various stages of flows, and running the automatic trash sweep.
Fish screens operations would occur every day when diversions are occurring. Operations include visually inspecting screens, verifying flow, clearing obstructions and debris, adjusting the baffles, permitting and regulatory compliance measures, estimating performance (i.e., velocity measurements), powering the screen, running the pumps for the sediment removal system, running automatic brush cleaning and trash rake motors, and running pumps for the fish diversion pipe. Operations also include methods to reduce predation of juvenile fish (e.g., noise systems to scatter predators, netting, and periodic draining of the screen return pipes).
Fish barrier operations would occur every day during salmon upmigration for spawning. Operations include visually inspecting screens, verifying flow, clearing obstructions and debris, installing and removing barrier screens, and permitting and regulatory compliance measures.
Fish passage facility operations would occur every day during fish migration. Operations include visually inspecting the facility, verifying flow, clearing obstructions and debris, adjusting the weirs, permitting and regulatory compliance measures, estimating performance (i.e., velocity measurements), powering mechanically controlled weirs.
There are no operations for the water diversion canal. Operation of the canal headworks is covered under control structures above.
Mendota Dam operations include placing and removing stop logs in order to operate the Short Canal (only applies to Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative; see Section 3.8).
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-19 – October 2012 San Joaquin River Restoration Program
3.4.13 Land Acquisition The approximate amount of additional lands to be acquired to accommodate the floodplain, levees, bypass channel, structures, and borrow was quantified based on parcel data in shapefile format from Fresno and Madera counties. Since portions of parcels outside the Project area may not be as easily utilized by the land owners, the entire parcels were considered, where appropriate, in the land acquisition costs for the Alternatives. The amount of land acquisition varies with each Alternative (approximately 2,450 to 3,300 acres).
3.4.14 Phased Implementation The Project may utilize a phased approach to implementation or construction of the selected alternative. Phased implementation would involve building selected components of the Project in separate construction phases, allowing Project funding to be secured over time. For example, the bypass channel and bifurcation structure could be built in a first phase, levees and floodplain construction in a second phase, and fish screens and fish passage facilities in a third phase. Exact phasing would be developed during the detailed design phase of the selected alternative.
3.4.15 Monitoring and Management Plan A Monitoring and Management Plan will be included in the Project EIS/R. Some components of the Project’s Monitoring and Management Plan would be covered by the Program’s Physical Monitoring and Management Plan (PEIS/R Appendix D.1, SJRRP 2011). The Project’s monitoring activities are summarized here.
The Monitoring and Management Plan will provide guidelines for observing conditions as well as adjusting to changes in physical conditions within the Project area. The Monitoring and Management Plan will consist of multiple component plans, addressing physical conditions such as flow, groundwater seepage, channel capacity, and propagation of native vegetation, as well as addressing effectiveness monitoring of fish screens and fish passage at structures. Each component plan will identify objectives for the physical conditions within the Project area, and provides guidelines for the monitoring and management of those conditions. The component plans identify potential actions that could be taken to further enhance the achievement of the objectives. Finally, the Plan will include a description of monitoring activities which apply to one or more of the component plans. The component plans will include the following:
• Flow – To ensure compliance with the hydrograph releases in Exhibit B of the Settlement and any other applicable flow releases (e.g., Buffer Flows) (part of the Program’s Physical Monitoring and Management Plan)
• Seepage – To reduce or avoid adverse or undesirable seepage impacts (part of the Program’s Physical Monitoring and Management Plan)
• Channel capacity – To maintain flood conveyance capacity (part of the Program’s Physical Monitoring and Management Plan)
Mendota Pool Bypass and Reach 2B Improvements Project 3-20 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
• Native vegetation – To establish and maintain native riparian habitat (part of the Program’s Physical Monitoring and Management Plan)
• Passage and screening effectiveness – To maintain effective fish passage and fish screening at structures and diversions
Monitoring Activities Monitoring activities would include physical and nonphysical activities within the Project area. Monitoring activities, as they will be described in the Monitoring and Management Plan, are guidelines for monitoring and could change as part of implementation of the Project. These activities could include the following:
• Flow monitoring – Flow, cross sections, and surface water stage at six gaging stations, and at additional locations during high-flow events (part of the Program’s Physical Monitoring and Management Plan)
• Groundwater level monitoring – Groundwater elevation in monitoring wells (part of the Program’s Physical Monitoring and Management Plan)
• Aerial and topographic surveys – True color aerial photographs and topographic surveys to assess river stage, hydraulic roughness, river width, bed elevation, and vegetation conditions (part of the Program’s Physical Monitoring and Management Plan)
• Vegetation surveys – Surveys of seed dispersal start and peak times, and native riparian vegetation establishment (part of the Program’s Physical Monitoring and Management Plan)
• Sediment mobilization monitoring – Sediment mobilization, bar formation, and bank erosion through aerial and topographic surveys of areas with elevated erosion potential (part of the Program’s Physical Monitoring and Management Plan)
• Passage and screening effectiveness – flow, cross-sections, water surface, and velocity measurements near and within structures that provide passage or screening. Fish counting devices and rotary screw traps to count and measure fish passage and fish size.
3.4.16 Conservation Strategy As part of Project implementation, a comprehensive strategy for the conservation of listed and sensitive species and habitats has been prepared, and would be implemented in coordination with USFWS, NMFS, and DFG. The strategy’s purpose is to serve as a tool built into the project description to minimize and avoid potential impacts to sensitive species and habitats. This Conservation Strategy guides development and implementation of specific conservation measures for project-level actions. The Conservation Strategy includes conservation goals and measures for species and communities (such as avoidance, minimization, monitoring, and management measures) consistent with adopted recovery plans, as described below. If avoidance and minimization measures are
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-21 – October 2012 San Joaquin River Restoration Program
impractical or infeasible, then further consultation actions and mitigation measures will be pursued and developed in coordination with the appropriate regulatory agency.
To achieve the Restoration Goal, a number of actions that are proposed to be implemented may substantially alter not only the aquatic ecosystem of the San Joaquin River, but also the river's riparian and wetland ecosystems, and some adjacent upland ecosystems. Riparian, wetland, and upland ecosystems of the Central Valley, such as those along the San Joaquin River, provide habitat for a large number of species, including several Federally-listed and State-listed species. Therefore, the action alternatives include this Conservation Strategy, which would be implemented in a manner that is consistent with adopted conservation plans for sensitive species, and for wetland and riparian ecosystems of the Restoration Area.
The Conservation Strategy consists of management actions that would result in a net benefit for riparian and wetland habitats in the Project area, to avoid reducing the long- term viability of sensitive species, and to be consistent with adopted conservation plans. The goals of the strategy are described below:
• Conserve riparian vegetation and waters of the United States, including wetlands – It is anticipated that implementing the Project would result in a net increase in the acreage of riparian and wetland vegetation in the Project area. However, several project actions may disturb or eliminate riparian vegetation or waters of the United States (including wetlands). If impacts to waters of the United States (including wetlands), navigable waters, or the Federal levee system cannot be avoided, a USACE Section 404, Section 408, and/or Section 10 permit and Central Valley Regional Water Quality Control Board (RWQCB) Section 401 water quality certification would be obtained. Increased acreage of wetlands resulting from Interim and Restoration flows may be considered a means of replacing, restoring, or enhancing wetlands. However, the acreage, location, and methods of replacing, restoring, or enhancing wetlands would be determined during these permitting processes. • Control and manage invasive species – Because of their adverse effects on aquatic and riparian ecosystems, the spread of invasive plant species as a result of Project would be controlled and managed. For each invasive plant species with known infestations, thresholds for management responses and specific management responses would be established and implemented (including species- specific control methods). • Conserve special-status species – Populations of special-status species would benefit from restoring and sustaining riparian and wetland habitat, and controlling invasive species, as described previously. However, during construction-related activities, a variety of special-status species of upland, wetland, and riparian habitats could experience adverse effects. Therefore, this strategy includes measures to prevent or reduce impacts that could result from loss of habitat within project footprints or from impacts on adjacent habitat or species. In addition, this strategy includes coordination with appropriate regulatory agencies to provide mitigation or compensation, consistent with applicable conservation plans, to
Mendota Pool Bypass and Reach 2B Improvements Project 3-22 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
avoid or minimize effects when actions would result in a net loss of habitat or other substantial adverse effects, if the implementation of avoidance and minimization measures is infeasible or impractical. These measures address all potentially affected Federally-listed and/or State-listed species, and all other species identified by USFWS, NMFS, or DFG as candidates, sensitive, or special-status in local or regional plans, policies, or regulations. For individual actions under each of the Project Alternatives, the applicable, feasible measures would guide development of action-specific conservation strategies. Table 3-2 presents the Conservation Strategy.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-23 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier
Vernal pool habitats, fleshy (succulent) owl’s clover, San Joaquin Valley VP Orcutt grass, hairy Orcutt grass, longhorn fairy shrimp, vernal pool fairy shrimp, and western spadefoot toad VP-1. Avoid a) If vernal pools or vernal pool species are anticipated within a project USFWS effects to area, a qualified biologist will identify and map vernal pool and DFG species seasonal wetland habitat potentially suitable for listed vernal pool plants, invertebrates, and western spadefoot toad within the project footprint. b) Facility construction and other ground-disturbing activities will be sited to avoid core areas identified in the Vernal Pool Recovery Plan (USFWS 2005) because conservation of these areas is a high priority for recovering listed vernal pool species. VP-2. Minimize a) If vernal pools are present, a buffer around the microwatershed or a Lead Agency effects to 250-foot-wide buffer, whichever is greater, will be established before species ground-disturbing activities around the perimeter of vernal pools and seasonal wetlands that provide suitable habitat for vernal pool crustaceans or vernal pool plants. This buffer will remain until ground- disturbing activities in that area are completed. Suitable habitat and buffer areas will be clearly identified in the field by staking, flagging, or fencing. b) Appropriate fencing will be placed and maintained around all preserved vernal pool habitat buffers during ground-disturbing activities to prevent impacts from vehicles and other construction equipment. c) Worker awareness training and on-site biological monitoring will occur during ground-disturbing activities to ensure buffer areas are being maintained. VP-3. a) If activities occur within the microwatershed or 250-foot-wide buffer USFWS Compensate for vernal pool habitat will be affected by the SJRRP, the project DFG for temporary proponent will develop and implement a compensatory mitigation or permanent plan, consistent with the USACE and EPA April 10, 2008, Final Rule loss of habitat for Compensatory Mitigation for Losses of Aquatic Resources (33 CFR Parts 325 and 332 and 40 CFR Part 230) and other applicable regulations and rules at the time of implementation, that will result in no net loss of acreage, function, and value of affected vernal pool habitat. Unavoidable effects will be compensated through a combination of creation, preservation, and restoration of vernal pool habitat or purchase of credits at a mitigation bank approved by the applicable regulatory agency/agencies. b) Project effects and compensation will be determined in consideration of the Vernal Pool Recovery Plan goals for core areas, which call for 95 percent preservation for habitat in the Grasslands Ecological Area
Mendota Pool Bypass and Reach 2B Improvements Project 3-24 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier and Madera core areas, and 85 percent habitat preservation in the Fresno core area (USFWS 2005). c) Appropriate compensatory ratios for loss of habitat both in and out of core areas will be determined during coordination and consultation with USFWS and/or DFG, as appropriate. d) If off-site compensation includes dedication of conservation easements, purchase of mitigation credits, or other off-site conservation measures, the details of these measures will be and developed as part of the USFWS and/or DFG coordination and consultation process. The plan will include information on responsible parties for long-term management, holders of conservation easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. Any impacts that result in a compensation purchase will require an endowment for land management in perpetuity before any project groundbreaking activities. CH Critical habitat a) Designated critical habitats shall be identified and mapped. USFWS CH-1. Avoid b) All SJRRP actions will be designed to avoid direct and indirect and minimize adverse modifications to these areas. effects to c) Minimization measures, such as establishing and maintaining buffers critical habitat around areas of designated critical habitat, shall be implemented if avoidance is not feasible. a) If critical habitat may be adversely modified by the implementation of USFWS SJRRP actions, the area to be modified will be evaluated by a qualified biologist to determine the potential magnitude of the project effects (i.e., description of primary constituent elements present and quantification of those affected) at a level of detail necessary to satisfy applicable environmental compliance and permitting CH-2. requirements. Compensate b) Compensatory conservation measures developed through Section 7 for unavoidable consultation with USFWS will be implemented. If off-site adverse effects compensation includes dedication of conservation easements, on Federally purchase of mitigation credits, or other off-site conservation designated measures, the details of these measures will be included in and critical habitat developed as part of the USFWS consultation process. The plan will include information on responsible parties for long-term management, holders of conservation easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. Any impacts that result in a compensation purchase require an endowment for land management in perpetuity before any project groundbreaking activities.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-25 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier
CTS California tiger salamander a) If potential California tiger salamander habitat or species are USFWS anticipated within the project area, within 1 year before project DFG construction activities, a qualified biologist shall identify and map potential California tiger salamander habitat (areas within 1.3 miles of known or potential California tiger salamander breeding habitat) within the project footprint. One week before ground-disturbing activities, a qualified biologist will survey for and flag the presence of CTS-1. Avoid ground squirrel and gopher burrow complexes. Where burrow and minimize complexes are present, a 250-foot-wide buffer shall be placed to effects to avoid and minimize disturbance to the species. species b) Facility construction and other ground-disturbing activities shall be sited to avoid areas of known California tiger salamander habitat and avoidance buffers. c) To eliminate an attraction to predators of the California tiger salamander, all food-related trash items such as wrappers, cans, bottles, and food scraps, must be disposed of in closed containers and removed at least once every day from the entire project site. a) Before and during construction activities, construction exclusion USFWS fencing will be installed just outside the work limit or around vernal pools where California tiger salamander may occur. This fencing shall be maintained throughout construction and will be removed at the conclusion of ground-disturbing activities. No vehicles will be allowed beyond the exclusion fencing. A USFWS-approved biological monitor shall be present on site, during intervals recommended by USFWS, to inspect the fencing. b) The biological monitor will be on site each day during any wetland restoration or construction, and during initial site grading or development of sites where California tiger salamanders have been CTS-2. found. Minimize c) Before the start of work each day, the biological monitor will check for effects to animals under any equipment to be used that day, such as vehicles species or stockpiles of items such as pipes. If California tiger salamanders are present, they will be allowed to leave on their own, before the initiation of construction activities for the day. To prevent inadvertent entrapment of California tiger salamanders during construction, all excavated, steep-walled holes or trenches more than 1 foot deep shall be covered, by plywood or similar materials, at the close of each working day or provided with one or more escape ramps constructed of earth fill or wooden planks. Before such holes or trenches are filled, they must be thoroughly inspected for trapped animals. d) Plastic monofilament netting (erosion control matting) or similar material shall not be used at the project site because California tiger salamanders may become entangled or trapped. Acceptable
Mendota Pool Bypass and Reach 2B Improvements Project 3-26 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier substitutes include coconut coir matting or tackified hydroseeding compounds. e) All ground-disturbing work shall occur during daylight hours. Clearing and grading will be conducted between April 15 and October 15, in coordination with USFWS and DFG, and depending on the level of rainfall and site conditions. f) Revegetation of project areas temporarily disturbed by construction activities will be conducted with locally occurring native plants. a) If California tiger salamander, or areas within 1.3 miles of known or USFWS potential California tiger salamander breeding habitat, would be DFG affected by the SJRRP, the project proponent will develop and implement a compensatory mitigation plan in coordination with USFWS and DFG, as appropriate. Unavoidable effects will be compensated through a combination of creation, preservation, and restoration of habitat or purchase of credits at a mitigation bank CTS-3. approved by the regulatory agencies. Compensate b) If off-site compensation includes dedication of conservation for temporary easements, purchase of mitigation credits, or other off-site or permanent conservation measures, the details of these measures will be loss of habitat included in and developed as part of the USFWS and/or DFG coordination and consultation process. The plan will include information on responsible parties for long-term management, holders of conservation easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. Any impacts that result in a compensation purchase will require an endowment for land management in perpetuity before any project groundbreaking activities. PALM Palmate-bracted bird’s beak a) If palmate-bracted bird’s beak is anticipated within the project area, a USFWS qualified botanist will identify and map the location of palmate-bracted DFG bird’s beak plants within the project footprint, within 1 year before the start of activities that may cause disturbance from either release of flows over 1,660 cfs or from ground-disturbing actions. PALM-1. Avoid b) A minimum 500-foot-wide buffer shall be placed around occurrences and minimize of palmate-bracted bird’s beak during construction activities, effects to consistent with recommendations in the Recovery Plan for Upland species Species of the San Joaquin Valley, California (USFWS 1998). The 500-foot-wide buffer will be clearly identified in the field by staking, flagging, or fencing. Project activity will avoid buffer areas, and work awareness training and biological monitoring will be conducted to ensure that the buffer area is not encroached on and that effects are being avoided.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-27 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier a) A compensatory conservation plan shall be developed in coordination USFWS with USFWS and DFG, as appropriate. The conservation plan will DFG require the project proponent to maintain viable plant populations in the Restoration Area and will identify compensatory measures for any populations affected. The conservation plan shall include monitoring and reporting requirements for populations to be preserved in or adjacent to construction areas, or populations to be protected or enhanced off site. b) If relocation efforts are part of the conservation plan, the plan will PALM-2. include details on the methods to be used: collection, Compensate relocation/transplant potential, storage, propagation, preparation of for temporary receptor site, installation, long-term protection and management, or permanent monitoring and reporting requirements, and remedial action loss of responsibilities should the initial effort fail to meet compensation occupied requirements. habitat c) If off-site compensation includes dedication of conservation easements, purchase of mitigation credits, or other off-site conservation measures, the details of these measures will be included in the conservation plan and must occur with full endowment for management in perpetuity before groundbreaking. The plan will include information on responsible parties for long-term management, holders of conservation easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. VELB Valley elderberry longhorn beetle a) If elderberry shrubs and valley elderberry longhorn beetle are USFWS anticipated within the project area, within 1 year before the commencement of ground-disturbing activities, a qualified biologist shall identify any elderberry shrubs in the project footprint. Qualified biologist(s) will survey potentially affected shrubs for valley elderberry VELB-1. Avoid longhorn beetle exit holes in stems greater than 1 inch in diameter. and minimize b) If elderberry shrubs are found on or adjacent to the construction effects to project site, a 100-foot-wide avoidance buffer – measured from the species dripline of the plant – will be established around all elderberry shrubs with stems greater than 1 inch in diameter at ground level and will be clearly identified in the field by staking, flagging, or fencing. No activities will occur within the buffer areas and worker awareness training and biological monitoring will be conducted to ensure that avoidance measures are being implemented. VELB -2. a) The project proponent will consult with USFWS to determine USFWS Compensate appropriate compensation ratios. Compensatory mitigation measures for temporary will be consistent with the Conservation Guidelines for Valley or permanent Elderberry Longhorn Beetle (USFWS 1999a), or current guidance. loss of habitat b) Compensatory mitigation for adverse effects may include
Mendota Pool Bypass and Reach 2B Improvements Project 3-28 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier transplanting elderberry shrubs during the dormant season (November 1 to February 15), if feasible, to an area protected in perpetuity, as well as required additional elderberry and associated native plantings and approved by USFWS. c) If off-site compensation includes dedication of conservation easements, purchase of mitigation credits, or other off-site conservation measures, the details of these measures will be included in the mitigation plan and must occur with full endowments for management in perpetuity. The plan will include information on responsible parties for long-term management, holders of conservations easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. BNLL Blunt-nosed leopard lizard BNLL-1. Avoid a) Three areas have been identified as having potential blunt-nosed USFWS and minimize leopard lizard habitat based on aerial maps. These areas include DFG effects to approximately 2,460 acres along the southwest side of the San species Joaquin River in Reach 2, approximately 490 acres in a portion of the Eastside Bypass and adjacent lands near Reach 4A of the San Joaquin River, and approximately 2,938 acres encompassing the northern side of the Mariposa Bypass and parcels north of the Mariposa Bypass and west of the Eastside Bypass. Within 1 year before the commencement of the proposed project, focused site visits and habitat assessment will be conducted on these lands. Based on focused assessment, and discussions with the USFWS and DFG, protocol-level surveys may be conducted. If blunt-nosed leopard lizard are detected within or adjacent to the project site, measures that will avoid direct take of this species will be developed in cooperation with USFWS and DFG and implemented before ground disturbing activities. (DWR 2010). BNLL-2. a) Compensation for impacts to the species, if needed, will be USFWS Compensate determined in coordination with USFWS and DFG as appropriate. DFG for temporary or permanent loss of habitat or species PLANTS Other special-status plants PLANTS-1. a) Within 1 year before the commencement of ground-disturbing USFWS Avoid and activities, habitat assessment surveys for the special-status plants DFG minimize listed in Table 1 of Appendix L of this Draft PEIS/R, “Biological effects to Resources – Vegetation and Wildlife,” will be conducted by a qualified special-status botanist, in accordance with the most recent USFWS and DFG plants guidelines and at the appropriate time of year when the target
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-29 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier species would be in flower or otherwise clearly identifiable. b) Locations of special-status plant populations will be clearly identified in the field by staking, flagging, or fencing a minimum 100-foot-wide buffer around them before the commencement of activities that may cause disturbance. No activity shall occur within the buffer area, and worker awareness training and biological monitoring will be conducted to ensure that avoidance measures are being implemented. c) Some special-status plant species are annual plants, meaning that a plant completes its entire life cycle in one growing season. Other special-status plant species are perennial plants that return year after year until they reach full maturity. Because of the differences in plant life histories, all general conservation measures will be developed on a case-by-case basis and will include strategies that are species- and site-specific to avoid impacts to special-status plants. a) USFWS and/or DFG will be consulted to determine appropriate USFWS compensation measures for the loss of special-status plants, as DFG appropriate. b) Appropriate mitigation measures may include the creation of off-site populations through seed collection or transplanting, preservation and PLANTS-2. enhancement of existing populations, restoration or creation of Compensate suitable habitat, or the purchase of credits at a regulatory-agency- for temporary approved mitigation bank. If off-site compensation includes or permanent dedication of conservation easements, purchase of mitigation credits, loss of special- or other off-site conservation measures, the details of these status plants measures will be included in the mitigation plan and must occur with full endowments for management in perpetuity. The plan will include information on responsible parties for long-term management, holders of conservations easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. GGS Giant garter snake a) If giant garter snake habitat is anticipated to be present within the Lead Agency project area, preconstruction surveys will be completed by a qualified USFWS biologist approved by USFWS and DFG within a 24-hour period DFG before any ground disturbance of potential giant garter snake habitat. GGS-1. Avoid If construction activities stop on the project site for a period of 2 and minimize weeks or more, a new giant garter snake survey will be completed no loss of habitat more than 24 hours before the restart of construction activities. for giant garter Avoidance of suitable giant garter snake habitat, as defined by snake USFWS (USFWS 1993) and DFG, will occur by demarcating and maintaining a 300-foot-wide buffer around these areas. b) For projects within potential giant garter snake habitat, all activity involving disturbance of potential giant garter snake habitat will be
Mendota Pool Bypass and Reach 2B Improvements Project 3-30 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier restricted to the period between May 1 and October 1, the active season for giant garter snakes. The construction site shall be re- inspected if a lapse in construction activity of 2 weeks or greater has occurred. c) Clearing will be confined to the minimal area necessary to facilitate construction activities. Giant garter snake habitat within or adjacent to the project will be flagged, staked, or fenced and designated as an Environmentally Sensitive Area. No activity shall occur within this area, and USFWS-approved worker awareness training and biological monitoring will be conducted to ensure that avoidance measures are being implemented. Construction activities shall be minimized within 200 feet of the banks of giant garter snake habitat. Movement of heavy equipment will be confined to existing roadways to minimize habitat disturbance. d) Vegetation shall be hand-cleared in areas where giant garter snakes are suspected to occur. Exclusionary fencing with one-way exit funnels shall be installed at least 1 month before activities to allow the species to passively leave the area and to prevent reentry into work zones, per USFWS and/or DFG guidance. e) If a giant garter snake is found during construction activities, USFWS, DFG, and the project’s biological monitor will immediately be notified. The biological monitor, or his/her assignee, will stop construction in the vicinity of the find and allow the snake to leave on its own. The monitor will remain in the area for the remainder of the work day to ensure the snake is not harmed. Escape routes for giant garter snake should be determined in advance of construction and snakes will be allowed to leave on their own. If a giant garter snake does not leave on its own within 1 working day, USFWS and DFG will be consulted. f) All construction-related holes shall be covered to prevent entrapment of individuals. Where applicable, construction areas shall be dewatered 2 weeks before the start of activities to allow giant garter snakes and their prey to move out of the area before any disturbance. a) Temporarily affected giant garter snake aquatic habitat will be USFWS restored in accordance with criteria listed in the USFWS Mitigation DFG Criteria for Restoration and/or Replacement of Giant Garter Snake Habitat (Appendix A to Programmatic Formal Consultation for U.S. GGS-2. Army Corps of Engineers 404 Permitted Projects with Relatively Compensate Small Effects on the Giant Garter Snake Within Butte, Colusa, Glenn, for temporary Fresno, Merced, Sacramento, San Joaquin, Solano, Stanislaus, or permanent Sutter, and Yolo Counties, California (USFWS 1997)), or the most loss of habitat current criteria from USFWS or DFG. b) Permanent loss of giant garter snake habitat will be compensated at a ratio and in a manner consulted on with USFWS and DFG. Compensation may include preservation and enhancement of
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-31 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier existing populations, restoration or creation of suitable habitat, or purchase of credits at a regulatory-agency-approved mitigation bank in sufficient quantity to compensate for the effect. Credit purchases, land preservation, or land enhancement to minimize effects to giant garter snakes should occur geographically close to the impact area. If off-site compensation is chosen, it shall include dedication of conservation easements, purchase of mitigation credits, or other off- site conservation measures, and the details of these measures will be included in the mitigation plan and must occur with full endowments for management in perpetuity. The plan will include information on responsible parties for long-term management, holders of conservations easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. WPT Western pond turtle a) A qualified biologist will conduct surveys in aquatic habitats to be DFG dewatered and/or filled during project construction. Surveys will be WPT-1. Avoid conducted immediately after dewatering and before fill of aquatic and minimize habitat suitable for western pond turtles. If western pond turtles are loss of found, the biologist will capture them and move them to nearby individuals USFWS- and/or DFG-approved areas of suitable habitat that will not be disturbed by project construction. EAGLE Bald eagle and golden eagle a) Surveys for bald and golden eagle nests will be conducted within 2 USFWS miles of any proposed project within areas supporting suitable nesting DFG habitat and important eagle roost sites and foraging areas. These surveys will be conducted in accordance with the USFWS Protocol for Evaluating Bald Eagle Habitat and Populations in California and DFG EAGLE-1. Bald Eagle Breeding Survey Instructions or current guidance Avoid and (USFWS Draft Project Design Criteria and Guidance for Bald and minimize Golden Eagles). effects to bald b) If an active eagle’s nest is found, project disturbance will not occur and golden within ½ mile of the active nest site during the breeding season eagles (as (typically December 30 to July 1) or any project disturbance if it is defined in the shown to disturb the nesting birds. A no-disturbance buffer will be Bald and established around the nest site for construction activities in Golden Eagle consultation with USFWS and DFG, and will depend on ecological Protection Act) factors, including topography, surrounding vegetation, nest height, and distance to foraging habitat, as well as the type and magnitude of disturbance. c) Project activity will not occur within the ½-mile-buffer areas, and worker awareness training and biological monitoring will be conducted to ensure that avoidance measures are being
Mendota Pool Bypass and Reach 2B Improvements Project 3-32 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier implemented. SWH Swainson’s hawk a) Preconstruction surveys for active Swainson’s hawk nests will be DFG conducted in and around all potential nest trees within 0.5 miles of project-related disturbance (including construction-related traffic).. SWH-1. Avoid b) If known or active nests are identified through preconstruction and minimize surveys or other means, a ½ mile no-disturbance buffer shall be impacts to established around all active nest sites if construction cannot be Swainson’s limited to occur outside the nesting season (February 15 through Hawk September 15). c) Worker awareness training and biological monitoring will be conducted to ensure that avoidance measures are being implemented. a) If foraging habitat for Swainson’s hawk is removed in association with DFG project implementation, foraging habitat compensation will occur in coordination with DFG. Foraging habitat mitigation may consist of planting and establishing alfalfa, row crops, pasture, or fallow fields. b) If potential nesting trees are to be removed during construction activities, removal will take place outside of Swainson’s hawk nesting season, and the project proponent will develop a plan to replace SWH-2. known Swainson’s hawk nest trees with a number of equivalent Compensate native trees that were previously determined to be impacts through for loss of nest consultation with DFG. Compensation shall include dedication of trees and conservation easements, purchase of mitigation credits, or other off- foraging habitat site conservation measures, and the details of these measures will be included in the mitigation plan and must occur with full endowments for management in perpetuity. The plan will include information on responsible parties for long-term management, holders of conservations easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. RAPTOR Other nesting raptors a) Construction activity, including vegetation removal, will only occur DFG outside the typical breeding season for raptors (September 1 to February 14), if raptors are determined to be present. RAPTOR-1. b) Preconstruction surveys will be conducted by a qualified biologist in Avoid and areas of suitable habitat to identify active nests in the project minimize loss footprint. of individual c) If active nests are located in the project footprint, a no-disturbance raptors buffer will be established until a qualified biologist determines that the nest is no longer active. The size of the buffer shall be established by a qualified biologist in coordination with DFG based on the sensitivity of the resource, the type of disturbance activity, and nesting stage.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-33 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier No activity shall occur within the buffer area, and worker awareness training and biological monitoring will be conducted to ensure that avoidance measures are being implemented. RAPTOR-2. DFG Compensate a) Native trees removed during project activities will be replaced with an for loss of nest appropriate number of native trees, in coordination with DFG. trees MBTA Other birds protected by the Migratory Bird Treaty Act a) Native nesting birds will be avoided by not conducting project activity, USFWS including vegetation removal, during the typical breeding season DFG (February 1 to September 1), if species covered under the Migratory MBTA-1. Avoid Bird Treaty Act and Fish and Game Code Sections 3503, 3503.5, and and minimize 3513 are determined to be present. effects to b) An Avian Protection Plan shall be established in coordination with species USFWS and DFG. Any overhead utility companies within the project area, whose lines, poles, or towers may be moved in association with the project, will also be consulted as part of the Avian Protection Plan. BRO Burrowing owl a) Preconstruction surveys for burrowing owls will be conducted in areas DFG supporting potentially suitable habitat and within 30 days before the start of construction activities. If ground-disturbing activities are delayed or suspended for more than 30 days after the preconstruction survey, the site should be resurveyed. BRO-1. Avoid b) Occupied burrows shall not be disturbed during the breeding season loss of species (February 1 through August 31). A minimum 160-foot-wide buffer shall be placed around occupied burrows during the nonbreeding season (September 1 through January 31), and a 250-foot-wide buffer shall be placed around occupied burrows during the breeding season. Ground-disturbing activities shall not occur within the designated buffers. a) If a DFG-approved biologist can verify through noninvasive methods DFG that owls have not begun egg-laying and incubation, or that juveniles from occupied burrows are foraging independently and are capable of independent survival, a plan shall be coordinated with DFG to offset BRO-2. burrow habitat and foraging areas on the project site if burrows and Minimize foraging areas are taken by SJRRP actions. impacts to b) If destruction of occupied burrows occurs, existing unsuitable burrows species should be enhanced (enlarged or cleared of debris) or new burrows created. This should be done in consultation with DFG. c) Passive owl relocation techniques must be implemented. Owls should be excluded from burrows in the immediate impact zone within a 160-foot-wide buffer zone by installing one-way doors in burrow
Mendota Pool Bypass and Reach 2B Improvements Project 3-34 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier entrances. These doors shall be in place at least 48 hours before excavation to insure the owls have departed. d) The project area shall be monitored daily for 1 week to confirm owl departure from burrows before any ground-disturbing activities. e) Where possible, burrows should be excavated using hand tools and refilled to prevent reoccupation. Sections of flexible plastic pipe should be inserted into the tunnels during excavation to maintain an escape route for any animals inside the burrow. BAT Special-status bats a) If suitable roosting habitat for special-status bats will be affected by DFG project construction (e.g., removal of buildings, modification of bridges), surveys for roosting bats on the project site will be conducted by a qualified biologist. The type of survey will depend on the condition of the potential roosting habitat and may include visual surveys or use of acoustic detectors. Visual surveys may consist of a daytime pedestrian survey for evidence of bat use (e.g., guano) and/or an evening emergence survey for the presence or absence of bats. The type of survey will depend on the condition of the potential roosting habitat. If no bat roosts are found, then no further study is required. BAT-1. Avoid b) If evidence of bat use is observed, the number and species of bats and minimize using the roost will be determined. Bat detectors may be used to loss of species supplement survey efforts. c) If roosts are determined to be present and must be removed, the bats will be excluded from the roosting site before the facility is removed. A mitigation program addressing compensation, exclusion methods, and roost removal procedures will be developed in consultation with DFG before implementation. Exclusion methods may include use of one-way doors at roost entrances (bats may leave, but not reenter), or sealing roost entrances when a site can be confirmed to contain no bats. Exclusion efforts may be restricted during periods of sensitive activity (e.g., during hibernation or while females in maternity colonies are nursing young). a) The loss of each roost will be replaced, in consultation with DFG, and DFG may include construction and installation of bat boxes suitable to the BAT-2. bat species and colony size excluded from the original roosting site. Compensate Roost replacement will be implemented before bats are excluded for loss of from the original roost sites. Once the replacement roosts are habitat constructed and it is confirmed that bats are not present in the original roost sites, the structure may be removed.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-35 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier
SJAS San Joaquin (Nelson’s) antelope squirrel a) A 50-foot-wide minimum buffer shall be maintained from all small DFG mammal burrows of suitable size for San Joaquin antelope squirrel. b) If work is to occur within the 50-foot-wide buffer, a qualified, permitted biologist shall conduct focused visual surveys for San Joaquin antelope squirrel within a 500-foot-wide buffer of the work area. These surveys shall coincide with the squirrels’ most active season, April 1 to September 30, and shall be conducted only when air temperatures are between 20º to 30º C (68º to 86º F). Surveys should be conducted using daytime line transects with 10- to 30-meter SJAS-1. Avoid spacing. Focused live trapping may also be required, in coordination and minimize with DFG. If San Joaquin antelope squirrels are observed during loss of surveys, no vegetation or soil disturbance will be allowed within 50 individuals feet of occupied burrows or burrow systems until the individuals are determined to no longer be occupying the area, as determined by a qualified biologist. c) Focused surveys, which may involve live trapping, may be required, in coordination with DFG, as appropriate. Additional conservation measures may developed pending the results of surveys, and in consultation with DFG. d) Construction activities shall be conducted when they are least likely to affect the species (i.e., after the normal breeding season). This timing shall be coordinated with USFWS and DFG. SJAS-2: DFG Compensate for temporary a) Compensation for impacts to the species, if needed, will be or permanent determined in coordination with DFG, as appropriate. loss of habitat or species FKR Fresno kangaroo rat a) Preconstruction surveys will be conducted by a qualified biologist per USFWS USFWS and DFG survey methodology to determine if potential DFG burrows for Fresno kangaroo rat are present in the project footprint. Surveys will be conducted within 30 days before ground-disturbing activities. The biologist will conduct burrow searches by FKR-1. Avoid systematically walking transects, which shall be adjusted based on and minimize vegetation height and topography, and in coordination with USFWS effects to and DFG. Transects shall be used to identify the presence of species kangaroo rat burrows. When burrows are found within 100 feet of the proposed project footprint, focused live trapping surveys shall be conducted by a qualified and permitted biologist, following a methodology approved in advance by USFWS and DFG. Additional conservation measures may be developed pending the results of
Mendota Pool Bypass and Reach 2B Improvements Project 3-36 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier surveys, and in consultation with USFWS and DFG. b) Construction activities shall be conducted when they are least likely to affect the species (i.e., after the normal breeding season). This timing shall be coordinated with USFWS and DFG. FKR-2. Avoid USFWS a) Facility construction and modification and other restoration projects disturbance of shall be sited to avoid primary constituent elements of designated DFG designated critical habitat for Fresno kangaroo rat. critical habitat FKR-3: a) Compensation for impacts to the species, if needed, will be USFWS Compensate determined in coordination with DFG and USFWS, as appropriate. DFG for temporary or permanent loss of habitat or species SJKF San Joaquin kit fox a) A qualified biologist will conduct preconstruction surveys no less than USFWS 14 days and no more than 30 days before the commencement of DFG activities to identify potential dens more than 5 inches in diameter. The project proponent shall implement USFWS’ (1999b) Standardized Recommendations for Protection of San Joaquin Kit Fox Prior to or During Ground Disturbance. The project proponent will notify USFWS and DFG in writing of the results of the preconstruction survey within 30 days after these activities are completed. b) If dens are located within the proposed work area, and cannot be SJKF-1. Avoid avoided during construction activities, a USFWS-approved biologist and minimize will determine if the dens are occupied. effects to c) If occupied dens are present within the proposed work, their species disturbance and destruction shall be avoided. Exclusion zones will be implemented following the latest USFWS procedures (currently USFWS 1999b). d) The project proponent will notify USFWS and DFG immediately if a natal or pupping den is found in the survey area. The project proponent will present the results of preactivity den searches within 5 days after these activities are completed and before the start of construction activities in the area. e) Construction activities shall be conducted when they are least likely to affect the species (i.e., after the normal breeding season). This timing shall be coordinated with USFWS and DFG. a) The project proponent, in coordination with USFWS and DFG, will USFWS SJKF-2. determine if kit fox den removal is appropriate. If unoccupied dens Compensate DFG need to be removed, the USFWS-approved biologist shall remove for loss of these dens by hand-excavating them in accordance with USFWS habitat procedures (USFWS 1999b).
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-37 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier b) Additional conservation measures will be coordinated with USFWS and DFG, and may include replacing dens, installing off-site artificial dens, acquiring compensation habitat, or other options to be determined. Compensation may include dedicating conservation easements, purchasing mitigation credits, or other off-site conservation measures, and the details of these measures will be included in the mitigation plan and must occur with full endowments for management in perpetuity. The plan will include information on responsible parties for long-term management, holders of conservations easements, long-term management requirements, and other details, as appropriate, for the preservation of long-term viable populations. c) The project proponent will present the results of den excavations to USFWS and DFG within 5 days after these activities are completed. PL Pacific lamprey a) A qualified biologist will conduct preconstruction surveys as outlined USFWS in Attachment A of USFWS’ Best Management Practices to Minimize Adverse Effects to Pacific Lamprey (Entosphenus tridentatus) (2010). PL-1. Avoid b) Work in documented areas of Pacific lamprey presence will be timed and minimize to avoid in-channel work during typical lamprey spawning (March 1 to effects to July 1). species c) If temporary dewatering in documented areas of lamprey presence is required for instream channel work, salvage methods shall be implemented to capture and move ammocoetes to a safe area, in consultation with USFWS. RHSNC Riparian habitat and other sensitive natural communities a) Biological surveys will be conducted to identify, map, and quantify DFG RHSNC-1. riparian and other sensitive habitats in potential construction areas. Avoid and b) Construction activities will be avoided in areas containing sensitive minimize loss natural communities, as appropriate. of riparian c) If effects occur to riparian habitat, emergent wetland, or other habitat and sensitive natural communities associated with streams, the State lead other sensitive agency will comply with Section 1602 of the California Fish and Game natural Code; compliance may include measures to protect fish and wildlife communities resources during the project. RHSNC-2. a) The Riparian Habitat Mitigation and Monitoring Plan for the SJRRP DFG Compensate will be developed and implemented in coordination with DFG. Credits for loss of for increased acreage or improved ecological function or riparian and riparian habitat wetland habitats resulting from the implementation of SJRRP actions and other will be applied as compensatory mitigation before additional sensitive compensatory measures are required. natural b) If losses of other sensitive natural communities (e.g., recognized as communities sensitive by CNDDB, but not protected under other regulations or
Mendota Pool Bypass and Reach 2B Improvements Project 3-38 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier policies) would not be offset by the benefits of the SJRRP, then additional compensation will be provided through creating, restoring, or preserving in perpetuity in-kind communities at a sufficient ratio for no net loss of habitat function or acreage. The appropriate ratio will be determined in consultation with USFWS or DFG, depending on agency jurisdiction. WUS Waters of the United States/waters of the State a) Before SJRRP actions that may affect waters of the United States or USACE waters of the State, Reclamation will map the distribution of wetlands (including vernal pools and other seasonal wetlands) in the Eastside and Mariposa bypasses. b) The project proponent will determine, based on the mapped distribution of these wetlands and hydraulic modeling and field observation, the acreage of effects, if any, on waters of the United WUS-1. Identify States. and quantify c) If it is determined that vernal pools or other seasonal wetlands will be wetlands and affected by the SJRRP, the project proponent will conduct a other waters of delineation of waters of the United States, and submit the delineation the United to USACE for verification. The delineation will be conducted States according to methods established in the USACE Wetlands Delineation Manual (Environmental Laboratory 1987) and Arid West Supplement (Environmental Laboratory 2008). d) Construction and modification of road crossings, control structures, fish barriers, fish passages, and other structures will be designed to minimize effects on waters of the United States and waters of the State, and will employ BMPs to avoid indirect effects on water quality. a) The project proponent, in coordination with USACE, will determine USACE the acreage of effects on waters of the United States and waters of the State that will result from implementation of the SJRRP. b) The project proponent will adhere to a “no net loss” basis for the WUS-2. Obtain acreage of wetlands and other waters of the United States and permits and waters of the State that will be removed and/or degraded. Wetland compensate for habitat will be restored, enhanced, and/or replaced at acreages and any loss of locations and by methods agreed on by USACE and the Central wetlands and Valley RWQCB, as appropriate, depending on agency jurisdiction. other waters of c) The project proponent will obtain Section 404 and Section 401 the United permits and comply with all permit terms. The acreage, location, and States/waters methods for compensation will be determined during the Section 401 of the State and Section 404 permitting processes. d) The compensation will be consistent with recommendations in the Fish and Wildlife Coordination Act Report (Appendix F of this Draft PEIS/R).
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-39 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier
INV Invasive plants a) Reclamation and the project lead agencies will implement the Lead Agency Invasive Vegetation Monitoring and Management Plan for the SJRRP (Appendix L of this Draft PEIS/R), which includes measures to monitor, control, and where possible eradicate, invasive plant INV-1. infestations during flow releases and construction activities. Implement the b) The implementation of the Invasive Vegetation Monitoring and Invasive Management Plan (Appendix L of this Draft PEIS/R) will include Vegetation monitoring procedures, thresholds for management responses, Monitoring and success criteria, and adaptive management measures for controlling Management invasive plant species. Plan c) The control of invasive weeds and other recommended actions in the Invasive Vegetation Monitoring and Management Plan (Appendix L of this Draft PEIS/R) will be consistent with recommendations in the Fish and Wildlife Coordination Act Report (Appendix F of this Draft PEIS/R). CP Conservation plans a) Facility siting and construction activities will be conducted in a USFWS CP-1. Remain manner consistent with the goals and strategies of adopted habitat consistent with DFG conservation plans, natural community conservation plans, or other approved approved local, regional, or State habitat conservation plans to the conservation extent feasible. Coordination shall occur with USFWS and/or DFG, plans as appropriate. CP-2. USFWS Compensate DFG effects a) The project proponent shall compensate effects consistent with consistent with applicable conservation plans and implement all applicable measures approved required by the plans. conservation plans GS Southern distinct population segment of North American green sturgeon a) The SJRRP will be operated in such a way that actions within green NMFS GS-1. Avoid sturgeon habitat shall be done in accordance with existing operating and minimize criteria of the CVP and SWP, and prevailing and relevant laws, loss of habitat regulations, BOs, and court orders in place when the action(s) are and individuals performed. CVS Central Valley steelhead a) Impacts to habitat conditions (i.e., changes in flows potentially NMFS CVS-1. Avoid resulting in decreased flows in the tributaries, increases in loss of habitat temperature, increases in pollutant concentration, change in and risk of take recirculation/recapture rates and methods, decrease in floodplain of species connectivity, removal of riparian vegetation, decreased in quality
Mendota Pool Bypass and Reach 2B Improvements Project 3-40 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier rearing habitat, etc.) must be analyzed in consultation with NMFS. b) The Hills Ferry Barrier will be operated and maintained to exclude Central Valley steelhead from the Restoration Area during construction activities and until suitable habitat conditions are restored. c) Maintenance of conservation measures will be conducted to the extent necessary to ensure that the overall long-term habitat effects of the project are positive. d) Before implementation of site-specific actions, the action agency shall conduct an education program for all agency and contracted employees relative to the Federally listed species that may be encountered within the study area of the action, and required practices for their avoidance and protection. A NMFS-appointed representative shall be identified to employees and contractors to ensure that questions regarding avoidance and protection measures are addressed in a timely manner. e) Disturbance of riparian vegetation will be avoided to the greatest extent practicable. f) A spill prevention plan will be prepared describing measures to be taken to minimize the risk of fluids or other materials used during construction (e.g., oils, transmission and hydraulic fluids, cement, fuel) from entering the San Joaquin River or contaminating riparian areas adjacent to the river itself. In addition to a spill prevention plan, a cleanup protocol will be developed before construction begins and shall be implemented in case of a spill. g) Stockpiling of materials, including portable equipment, vehicles and supplies, such as chemicals, shall be restricted to the designated construction staging areas, exclusive of any riparian and wetland areas. h) A qualified biological monitor will be present during all construction activities, including clearing, grubbing, pruning, and trimming of vegetation at each job site during construction initiation, midway through construction, and at the close of construction, to monitor implementation of conservation measures and water quality. i) The San Joaquin River channel shall be designed to decrease or eliminate predator holding habitat, in coordination with NMFS. a) In-channel construction activities that could affect designated critical NMFS habitat for Central Valley steelhead will be limited to the low-flow CVS-2. period between June 1 and October 1 to minimize potential for Minimize loss adversely affecting Federally listed anadromous salmonids during of habitat and their emigration period. risk of take of b) In-channel construction activities that could affect designated critical species habitat for Central Valley steelhead will be limited to daylight hours during weekdays, leaving a nighttime and weekend period of passage for Federally listed fish species.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-41 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier c) Construction BMPs for off-channel staging, and storage of equipment and vehicles, will be implemented to minimize the risk of contaminating the waters of the San Joaquin River by spilled materials. BMPs will also include minimization of erosion and stormwater runoff, as appropriate. d) Riparian vegetation removed or damaged will be replaced at a ratio, coordinated with NMFS, within the immediate area of the disturbance to maintain habitat quality. e) If individuals of listed species are observed present within a project area, NMFS must be notified. NMFS personnel shall have access to construction sites during construction, and following completion, to evaluate species presence and condition and/or habitat conditions. f) If bank stabilization activities should be necessary, then such stabilization shall be constructed to minimize predator habitat, minimize erosion potential, and contain material suitable for supporting riparian vegetation. SRCS Central Valley spring-run Chinook salmon a) The SJRRP will be operated in such a way that actions in the vicinity NMFS of spring-run Chinook salmon habitat shall be done in accordance DFG SRCS-1. Avoid with existing operating criteria of the CVP and SWP, and prevailing and minimize and relevant laws, regulations, BOs, and court orders in place at the loss of habitat time the actions are performed. and individuals b) SJRRP actions shall be performed in accordance with the Experimental Population 4(d) rule, as it is developed, and where applicable. EFH Essential fish habitat (Pacific salmonids and starry flounder) a) Impacts to habitat conditions (e.g., changes in flows potentially NMFS resulting in decreased flows in the tributaries, increases in temperature, increases in pollutant concentration, change in recirculation/recapture rates and methods, decrease in floodplain connectivity, removal of riparian vegetation, decreased in quality rearing habitat) must be analyzed in consultation with NMFS. b) The Hills Ferry Barrier will be operated and maintained to exclude EFH-1. Avoid Pacific salmonids from the Restoration Area during construction loss of habitat activities, and until suitable habitat conditions are restored. and risk of take c) Maintenance of conservation measures will be conducted to the of species extent necessary to ensure that the overall long-term habitat effects of the project are positive. d) Before implementation of site-specific actions, the action agency shall conduct an education program for all agency and contracted employees relative to the Federally listed species that may be encountered within the study area of the action, and required practices for their avoidance and protection. A NMFS-appointed
Mendota Pool Bypass and Reach 2B Improvements Project 3-42 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier representative shall be identified to employees and contractors to ensure that questions regarding avoidance and protection measures are addressed in a timely manner. e) Disturbance of riparian vegetation will be avoided to the greatest extent practicable. f) A spill prevention plan will be prepared describing measures to be taken to minimize the risk of fluids or other materials used during construction (e.g., oils, transmission and hydraulic fluids, cement, fuel) from entering the San Joaquin River or contaminating riparian areas adjacent to the river itself. In addition to a spill prevention plan, a cleanup protocol will be developed before construction begins and shall be implemented in case of a spill. g) Stockpiling of materials, including portable equipment, vehicles and supplies, such as chemicals, shall be restricted to the designated construction staging areas, exclusive of any riparian and wetland areas. h) A qualified biological monitor will be present during all construction activities, including clearing, grubbing, pruning, and trimming of vegetation at each job site during construction initiation, midway through construction, and at the close of construction to monitor implementation of conservation measures and water quality. i) The bottom topography of the San Joaquin River channel will be designed to decrease or eliminate predator holding habitat. a) In-channel construction activities that could affect habitat for will be limited to the low-flow period between June 1 and October 1 to minimize potential for adversely affecting Federally listed anadromous salmonids during their emigration period. b) In-channel construction activities that could affect habitat for starry flounder and Pacific salmonids will be limited to daylight hours during weekdays, leaving a nighttime and weekend period of passage for EFH-2. Federally listed fish species. Minimize loss c) Construction BMPs for off-channel staging and storage of equipment of habitat and and vehicles will be implemented to minimize the risk of risk of take contaminating the waters of the San Joaquin River by spilled from materials. BMPs will also include minimization of erosion and implementation stormwater runoff, as appropriate. of construction d) Riparian vegetation removed or damaged will be replaced at a ratio, activities coordinated with NMFS, within the immediate area of the disturbance to maintain habitat quality. e) If individuals of listed species are observed present within a project area, NMFS must be notified. NMFS personnel shall have access to construction sites during construction and following completion to evaluate species presence and condition and/or habitat conditions. f) If bank stabilization activities should be necessary, then such stabilization shall be constructed to minimize predator habitat,
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-43 – October 2012 San Joaquin River Restoration Program
Table 3-2 Conservation Measures for Biological Resources That May Be Affected by Project Actions Conservation Applicable Habitat and/or Species, and Conservation Regulatory Measure and Measure Description Agency Identifier minimize erosion potential, and contain material suitable for supporting riparian vegetation.
Mendota Pool Bypass and Reach 2B Improvements Project 3-44 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.5 Compact Bypass with Narrow Floodplain and South Canal
The Compact Bypass with Narrow Floodplain and South Canal includes:
• Building levees capable of conveying flows up to 4,500 cfs with 3 feet of freeboard • Restoring floodplain habitat an average of approximately 3,000 feet wide to provide benefit to salmonids and other native fishes • Construction of a new channel and structures capable of conveying up to 4,500 cfs of Restoration Flows around the Mendota Pool • Construction of the South Canal and structures capable of conveying up to 2,500 cfs from Reach 2B to Mendota Pool • Providing upstream and downstream fish passage for adult and juvenile salmonids and other native fishes between Reach 2A and Reach 3 This Alternative would construct a channel between Reach 2B and Reach 3, the Compact Bypass Channel, in order to bypass the Mendota Pool. Restoration Flows would enter Reach 2B, flow through the reach, then downstream to Reach 3 via the Compact Bypass Channel. A canal to convey San Joaquin River water deliveries to Mendota Pool, the South Canal, would be built. The San Joaquin River control structure at the Chowchilla Bypass would be removed, and a bifurcation structure would be built at the head of the South Canal to control flood diversions into the Chowchilla Bypass and water delivery diversions into Mendota Pool. Fish passage facilities and a fish screen would be built at the South Canal bifurcation structure to provide passage around the structure and prevent fish being entrained in the diversion. A fish barrier would be built in Reach 3 to direct up-migrating fish into the Compact Bypass Channel. A new crossing would be built at the San Mateo Avenue crossing. These features are described in further detail in the sections below.
See Figure 3-4 and Figure 3-5 for a plan view of the Alternative’s features. In Section 3.6.8, Table 3-3, Table 3-4, and Table 3-5 list the quantities of levee construction, relocations, and land acquisition, costs, conditions, and features associated with this Alternative.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-45 – October 2012 San Joaquin River Restoration Program
Figure 3-4 Plan View of Compact Bypass with Narrow Floodplain and South Canal
Mendota Pool Bypass and Reach 2B Improvements Project 3-46 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Figure 3-5 Inset Map of Compact Bypass with Narrow Floodplain and South Canal
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-47 – October 2012 San Joaquin River Restoration Program
3.5.1 Fish Habitat and Passage The purpose of the floodplain would be to provide riparian and floodplain habitat and support the migration and seasonal rearing of salmonids and other native fishes in Reach 2B. The floodplain has an average width of approximately 3,000 feet and an inundated area of approximately 850 acres at 2,500 cfs.
This Alternative provides floodplain habitat resulting in approximately 450 acres of shallow water habitat for primary production7 as well as approximately 400 acres of habitat that supports direct rearing8 at 2,500 cfs. Approximately 55 percent of the floodplain in this Alternative would inundate less than 1 foot deep at 2,500 cfs. This Alternative also retains approximately 200 acres of shallow water habitat at flows up to 4,500 cfs. Source: Tetra Tech 2012 Figure 3-6 below presents conceptual inundation areas for primary production and rearing habitats as they vary by flow. Inundation acreages may change during the design process.
1200
1000
800
Depth of Inundation: 600
Acres Production <1ft 400 Rearing >1ft
200
0 1500 2000 2500 3000 3500 4000 4500 Flow (cfs)
Source: Tetra Tech 2012 Figure 3-6 Potential Inundation Acreage by Flow for Compact Bypass with Narrow Floodplain and South Canal
In the Compact Bypass channel, floodplain benches with an approximate average width of 300 feet on each side the main flow portion of the bypass channel are included (see Section 3.6.3). Riparian and floodplain habitat would develop on the benches in the
7 Primary production is defined as the production of organic compounds from atmospheric or aquatic carbon dioxide, principally through the process of photosynthesis. The organisms responsible for primary production are known as primary producers or autotrophs, and form the base of the food chain. 8 Juvenile salmon direct rearing habitat is defined as areas with water greater than 1.0 feet deep at 2,300 cfs, a flow which will occur in approximately one out of every two years for a sustained period of at least 20 days in the period March 15 to May 15 (see further discussion in Attachment A Section 6.2.2). The modeled flow of 2,500 cfs is used as a surrogate for 2,300 cfs.
Mendota Pool Bypass and Reach 2B Improvements Project 3-48 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
bypass channel to benefit migrating fish and promote a stable channel and sediment transport from Reach 2B to Reach 3.
This Alternative includes several facilities that fish would encounter or need to pass to migrate between Reach 3 and Reach 2B (from downstream to upstream):
• A fish barrier near the downstream end of the Compact Bypass • Several (10 to 18) in-channel drop structures in the Compact Bypass • The San Mateo Avenue crossing (this crossing is included in all Alternatives) • Four fish screen return outlets from the South Canal fish screen • A bifurcation control structure at the South Canal with fish passage facility • A fish screen near the upstream end of the South Canal • Fish screens at Lone Willow Slough, Big and Little Bertha pumps, and other smaller diversions (these screens are included in all Alternatives) Each structure would be designed to perform according to the fish passage design criteria (see Section 3.4.1). In addition, the channel and floodplain incorporate riparian plantings to provide cover, woody material, and velocity variability, while the design footprint allows sufficient space to incorporate channel structure variability during detailed design, all of which may help to reduce stress and predation.
This Alternative includes a fish barrier at the downstream end of the bypass channel to keep fish from migrating into false migration pathways. Without the barrier, a false migration pathway up to the base of Mendota Dam would be available to fish in all years, and a false migration pathway into Mendota Pool and Fresno Slough (potentially into the King River system) would occur in about one in five years, when the boards are taken out of Mendota Dam to pass Pine Flat flood releases into Reach 3. However, with the barrier, which would be designed to accommodate flows up to 4,500 cfs, fish would not be able to migrate to Mendota Dam or enter Mendota Pool, but they would be guided into the bypass channel and Reach 2B.
3.5.2 Floodplain and Riparian Habitat This Alternative includes passive riparian habitat restoration and farming in the floodplain. It is assumed that over time wetland communities (obligate, facultative-wet, and facultative species) would develop within the main channel and that a dense riparian scrubland would develop along the main river channel banks. Between the main river channel banks and the proposed levees, agricultural practices (e.g., annual crops, pasture, or floodplain-compatible permanent crops) would occur.9 The Restoration Flows would be used to recruit new vegetation along the channel. This Alternative relies upon existing seed banks (upstream of the Project and on portions of existing Reach 2B levees to
9 Rearing on floodplains with agricultural practices has been shown to provide faster salmon growth rates over in-channel rearing. (Sommer 2001)
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-49 – October 2012 San Joaquin River Restoration Program
remain) and Restoration Flows for vegetation recruitment. Invasive, non-native species would be removed from the channel and riparian areas during or following construction, and the Project would include long-term management for invasives.
Several native vegetation alliances may develop in the riparian areas, such as Saltgrass Flats, Sandbar Willow Thickets, California Mugwort Brush, Black Willow Thickets, Riparian Bank Herbs, California Bulrush Marsh, Button Willow Thickets, Oregon Ash Groves, Creeping Rye Grasslands, and Fremont Cottonwood Forests.
Maintenance and Invasive Species Control Invasive, non-native species would be removed from the Project area during the construction phase. Long-term management of the Project would consist of removal of the most invasive non-native species within the reach such as giant reed grass (Arundo donax), perennial pepperweed (Lepidium latifolium) and poison hemlock (Conium maculatum). Long-term management would also include removal of other invasive species that are currently found in upstream reaches and may eventually colonize in the Project area such as red sesbania (Sesbania punicea), salt cedar (Tamarix species), and Chinese tallow (Sapium sebiferum). Invasives removal techniques may include mechanical removal, root excavation, hand pulling, mowing, disking, controlled burning, grazing, aquatic-safe herbicides, or a combination of techniques as appropriate.
While it is not anticipated that major management actions would be needed, the key objective of long-term management would be to monitor and identify any environmental issues that arise, and use adaptive management to determine what actions would be most appropriate to correct these issues.
The general management approach to the long-term maintenance of the floodplain areas would be to maintain quality habitat for each natural resource, on-going monitoring and maintenance of key environmental characteristics of the entire floodplain area within the reach. An adaptive management approach would be used to incorporate changes to management practices, including corrective actions as determined to be appropriate by the Bureau of Reclamation. Adaptive management includes those activities necessary to address the effects of climate change, fire, flood, or other natural events, force majeure, etc.
The expected long-term management needs and activities necessary to maintain any on- site mitigation sites would be: resource specific long-term maintenance activities and other general maintenance activities such as exotic species elimination, grazing management, clean-up and trash removal, infrastructure management such as gate, fence, road, culvert, signage and drainage-feature repair, and other maintenance activities necessary to maintain the riparian and floodplain habitat quality.
Existing Native Vegetation Protection The existing native vegetation in the Project area designated to remain would be temporarily fenced with orange snow fencing (or equivalent) to prevent entry, driving, parking, or storing equipment or material within these areas during construction. Existing vegetation would be left in place or only minimally trimmed to facilitate access and work
Mendota Pool Bypass and Reach 2B Improvements Project 3-50 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
at the site. The existing soil is an ideal growing medium for all the desired native plants. In order to maximize plant growth and planting success, existing soil and topsoil would be preserved and disturbance during construction would be minimized to the maximum practicable extent.
3.5.3 Compact Bypass Channel The bypass channel would convey 4,500 cfs around the Mendota Pool by constructing a channel just southwest of the existing Columbia Canal alignment. Once constructed, the bypass channel would become the new river channel. This Alternative includes excavating the bypass channel, constructing levees and in-channel structures, removing existing levees, relocating or modifying existing infrastructure, and acquiring land. The in-channel structures may include bifurcation control structures, grade control structures, fish screen(s), fish passage facility(ies), fish barrier(s), Columbia Canal Siphon, as well as the Drive 10 ½ realignment and are discussed in Section 3.6.5. The bypass channel and associated structures provide upstream and downstream passage of juvenile Chinook salmon and upstream passage of adult Chinook salmon, as well as passage for other native fishes, while isolating Mendota Pool from Restoration Flows.
The bypass channel would connect to Reach 3 approximately 0.6 miles downstream from Mendota Dam (approximately RM 204), bypass the Mendota Pool to the north, and connect to Reach 2B approximately 0.9 miles upstream from Mendota Dam (approximately RM 205.5). The bypass channel would have a total length of approximately 0.9 miles. A siphon under the bypass channel would be constructed to connect the Columbia Canal to the Mendota Pool.
The bypass channel would be a multi-stage channel designed to facilitate fish passage at low flows, channel stability at moderate flows, and contain high flows. The low-flow channel would be designed for a capacity of around 200 cfs and would have a topwidth of approximately 110 feet and a depth of approximately 2 feet. The main channel would be designed for a capacity of around 1,860 cfs (approximately the 2-year annual peak Restoration Flow in Reach 2B) and would have an average topwidth of approximately 320 feet and total depth of approximately 6 feet. The floodplain bench would be designed with a shallow cross-slope (approximately 1 percent slope) to allow variable floodplain depths at flows between 1,860 cfs and 4,500 cfs.
The channel, designed as an unlined earthen channel, would be approximately 4,800 feet long with a total corridor width of approximately 950 feet. The average slope of the channel between grade control structures would be approximately 0.0004 (approximately 2.1 feet/mile), while the total elevation drop would be approximately 12 feet including grade control structures. A series of grade-control structures would be included to achieve the necessary elevation change (see Section 3.6.5).
3.5.4 South Canal The South Canal would deliver up to 2,500 cfs in water deliveries from the San Joaquin River to Mendota Pool (see Section 3.6.6). The South Canal could connect to the river at various locations, ideally on a straight section of the river or on the outside of bend. Two optional locations for the junction with the San Joaquin River are shown in Figure 3-4 at
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-51 – October 2012 San Joaquin River Restoration Program
approximately RM 214.2 and RM 215. The South Canal would discharge into Fresno Slough via the Little San Joaquin Slough approximately 2.3 river miles south of Mendota Dam.
Water deliveries would be controlled at the upstream end of the South Canal by a bifurcation structure. The river control structure would have a fish passage facility for fish passage, and the canal control structure would have a fish screen to prevent entrainment. The control structures, fish screen, and fish passage facilities are discussed in Section 3.6.5.
The South Canal could be concrete-lined or unlined. The unlined design would include maintained grasses in the channel. Either design would have a trapezoidal cross-section. The lined South Canal would have a top-width of approximately 90 feet, a total corridor width of approximately 180 feet (including levees and maintenance roads), and 2H to 1V side slopes on the canal banks and levees. The unlined South Canal would have a top- width of approximately 270 feet, total corridor width of approximately 490 feet (including levees and maintenance roads), and 3H to 1V side slopes on the canal banks and levees.
Levee heights would be based on a flow of 2,500 cfs and 3 feet of freeboard. Seepage control measures and erosion protection would be included as necessary to minimize seepage impacts and reduce erosion and scour in the canal. However, seepage is assumed to not be an issue for a lined canal, so seepage control measures would not be provided for the lined canal.
The South Canal would cross San Mateo Avenue, so a bridge crossing would be provided to maintain access. The bridge would include concrete deck, reinforcing steel, piles, and pile extensions, railing, excavation, and backfill.
3.5.5 Structures The structures described below would be required to provide the operational flexibility to divert water to the Mendota Pool, provide fish passage, allow maintenance access to Mendota Dam, prevent fish entrainment and straying, and provide controlled elevation drop between Reach 2B and Reach 3.
San Joaquin River Control Structure at Chowchilla Bypass Removal The existing Chowchilla Bifurcation Structure consists of two control structures: one at the head of the Chowchilla Bypass and one across the San Joaquin River at RM 216. With the inclusion of a bifurcation structure at the head of the South Canal, a new control structure would be built across the San Joaquin River at the head of the canal. The new control structure would alleviate the need for the San Joaquin River control structure at the Chowchilla Bypass because all diversions into the Chowchilla Bypass could be controlled from the new control structure at the head of the South Canal. As part of this Alternative, the San Joaquin River control structure at the Chowchilla Bypass would be demolished.
Mendota Pool Bypass and Reach 2B Improvements Project 3-52 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
South Canal Bifurcation Structure A bifurcation structure would be constructed at the upstream end of the South Canal. The bifurcation structure consists of two control structures: one across the path of Restoration Flows (San Joaquin River) and one across the path of water deliveries to Mendota Pool (South Canal).
The control structure across the path of the Restoration Flows would be designed to accommodate up to 4,500 cfs and consists of six 20-foot wide bays for a structure length of approximately 138 feet. Conditions in this control structure would be designed to meet NMFS 2001 and NMFS 2008 fish passage criteria when flow conditions are amenable. The control structure across the path of the water deliveries would be designed to accommodate up to 2,500 cfs and consists of four 20-foot wide bays for a structure length of approximately 93 feet. Flow through each bay would be controlled by a gate (e.g., radial (Tainter) or inflatable Obermeyer). In the final design, the number and size of the gates may be modified. The size of the gates would be determined by the design maximum flow.
The Restoration Flow path structure includes a fish passage facility on the side of the structure, and the water deliveries flow path structure includes a fish screen upstream of the structure. Each control structure would be placed in the middle of the channel and has earthen embankments connecting the structure to the proposed levees. The connector embankments may include culverts, gates, weirs, inflatable bladder dams, or other features to improve flow and fish passage on the floodplain when water deliveries are not occurring. A 16-foot wide roadway and 20-foot wide maintenance/operations platform would be provided over each control structure.
South Canal Fish Passage Facility The South Canal bifurcation structure would include a fish passage facility on the side of the control structure across the Restoration Flow path. The fish passage facility would be necessary to provide passage during Pool deliveries and for Restoration Flows where passage conditions through the control structure may not be ideal.
Passage Facility Design The design of the fish passage facility would be based on criteria in Anadromous Salmonid Passage Facility Design (NMFS 2008). The size and geometry of the fish passage facility would be dictated by the flow requirements for juvenile and adult fish in Table 3-1. Several types of fish passage facility may be considered in detailed design: vertical slot weir ladder design was included for its ability to accommodate a greater range of water depths (hydraulic head at the upstream and downstream ends), but the design may also consider ice-harbor, pool and chute, rock ramp fishway or other passage facility designs.
A roadway would need to be built over the fish passage facility to connect the maintenance road atop the river control structure with the levee road on the south side of the river. The roadway would be supported by the vertical concrete walls of the fish passage facility or other structural features.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-53 – October 2012 San Joaquin River Restoration Program
Attraction Flows The attraction flow magnitude will be 5 to 10 percent of the total flow through the control structure over the path of Restoration Flows. The Project requires conveyance of at least 4,500 cfs, so the attraction flow at the passage facility entrance could be as high as 450 cfs. The passage facility itself may have a design flow rate less than the maximum attraction flow. In this case, the balance of attraction flows would be provided at the passage facility entrance (downstream side) through supplementary water, described below.
Supplementary Water Supplementary water is water already in the river and which is piped to the fish passage facility entrance to augment attraction flows. No additional water supply beyond what would be flowing in the river is required. The supplementary water allows the passage facility to operate under a wider range of river flows by supplying additional attraction flow when the need exceeds the design flow rate through the passage facility. Supplementary water would also be used to control the hydraulic head at the passage facility entrance.
Supplementary flow would be collected by a water delivery intake structure located upstream from the fish passage facility (see Figure 3-7). The intake structure would include an automated cleaning system, trash rack and a fish screen to prevent migrating fish from entering the intake. River water would enter the intake structure, and travel downriver through pipes to the passage facility entrance.
RIVER CONTROL STRUCTURE
FLOW
ATTRACTION FLOW OUTLET
FLOW
FISH PASSAGE FACILITY
SUPPLEMENTAL FLOW INTAKE
Figure 3-7 Supplementary flow system plan-view diagram
South Canal Fish Screen A fish screen would be included at the head of the South Canal where Pool deliveries would be diverted from the river. The fish screen would be necessary to keep or return out-migrating juvenile salmon to the path of Restoration Flows during Pool deliveries.
Mendota Pool Bypass and Reach 2B Improvements Project 3-54 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
The screen would be designed to pass flow up to 2,500 cfs. The type of fish screen could be a fixed flat plate in “V” configuration, vertical flat plate, inclined flat plate, cone, or cylindrical screens. Depending on the design type, the fish screen facility may include trash racks, stainless steel wedge wire fish screens, flow control baffle systems behind the screens, screen cleaning systems for the trashracks and screens, bypass flow control weirs, fish-friendly pumps, and/or fish bypass pressure pipelines. The trash racks would be installed at the entrance to the screen structures to protect screens from trash, logs, and other large debris.
Approach, sweeping, and bypass entrance velocities would be kept within established fish screen criteria (NMFS 2008). Flow through the fish screens may be controlled by baffles behind the fish screens. Cleaning of the screens would be accomplished using an automated brush system. Electric power would be needed for fish friendly pumps, if included, and screen cleaning systems. Operation of the fish screens would include methods to reduce predation of juvenile fish (e.g., noise systems to scatter predators, netting, and periodic draining of the screen return pipes).
Replacement of San Mateo Avenue Crossing The San Mateo Avenue crossing is an existing river crossing located within a public right-of-way in Madera County and on private land in Fresno County at approximately RM 211.8. The crossing transitions from public right-of-way to private land at the center of the river. In order to maintain vehicular access, accommodate increased flow magnitudes associated with Restoration Flows, and provide fish passage, an improved crossing would be included with this Alternative. The crossing would accommodate the increased flows in the river by maintaining the required velocities for proper fish passage for flows up to 4,500 cfs. The crossing would be designed to meet NMFS 2001 and NMFS 2008 passage criteria. The crossing would be overtopped during some flows.
The proposed San Mateo Avenue crossing includes installing a low flow or dip crossing with multiple, counter-sunk concrete box culverts designed for highway loading. The structure includes armoring along the entrance and exit of the structure as well as along the channel banks in the immediate vicinity of the structure. The armoring would be necessary to protect the structure during overtopping flows. Culverts would be embedded below the existing channel bed. Grouted riprap would be placed in the culvert below the existing channel bed to prevent channel scour reaching the floor of the culvert and to create a roughened boundary layer for fish passage. Native bed material would be placed above the grouted riprap up to the existing channel bed elevation to provide passage conditions similar to that which exists in the adjacent natural stream.
Mendota Pool Dike Adjacent to the head of the Compact Bypass, a dike across the existing river channel would be needed to prevent water in the Pool from flowing into the Compact Bypass. The dike would be of similar design as the levees in Section 3.4.2 including seepage control measures to prevent seepage from the Pool into the Compact Bypass. The dike would run from the proposed Reach 2B levee on the south side of the river, across the river, to proposed left-bank levee of the Compact Bypass. This structure would likely be regulated by DWR Division of Safety of Dams (DSOD).
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-55 – October 2012 San Joaquin River Restoration Program
Drive 10 ½ The Compact Bypass would cross existing Drive 10 ½, which provides access to the east side of Mendota Dam. With this Alternative, the road would end at east side of the bypass channel and would not continue to Mendota Dam.
Mendota Dam Fish Barrier A fish exclusion barrier would be included in Reach 3 near the downstream end of the Compact Bypass to prevent adult fish from migrating beyond the bypass channel up to the base of Mendota Dam, which during most flows out of Mendota Pool, would be a dead end for fish passage. This would lead to delays in adult salmon migration or potentially death. Although out-migrating fish would not be expected to be present downstream from Mendota Dam, the fish barrier would allow juveniles to pass the structure.
The exclusion barrier design would be a high-flow picket barrier, which is a flow-through structure of closely spaced bars (i.e., pickets) that prevent adult fish from traveling upstream in the river to Mendota Dam at flows up to a combined discharge of 4,500 cfs (Mendota Dam and the Compact Bypass). The design accounts for a range of flow options from routing the entire 4,500-cfs flow through the structure (flood flows from the James Bypass), to routing a 600-cfs irrigation delivery through the structure with up to 3,900 cfs being routed down the Compact Bypass, to routing no flow through the structure with up to 4,500 cfs down the Compact Bypass.
The total length of the structure would be approximately 1,410 feet, with 260 feet across the main channel and 1,150 feet across the overbanks. The base of the structure would consist of a concrete sill connected to concrete piles, which extend into clay layers. The structure would be approximately 20 feet high in the main channel and 9 feet high in the overbanks. Riprap would be placed 2 feet thick at the entrance and exit of the sill to prevent erosion. The fish barrier meets the average through-velocity criteria of 1.0 fps in Anadromous Salmonid Passage Facility Design (NMFS 2008).
In order to meet velocity criteria for the structure, some floodplain grading between the existing Reach 3 levees would be required to provide even flow-through conditions. In addition, approximately 4,200 linear feet of improvements to the Reach 3 left-bank levee are included to ensure that backwater conditions at the structure do not affect adjacent property. The improved Reach 3 levee would have the same alignment as the existing levee.
Grade Control Structures A series of several (10 to 18), approximately 0.5-ft high grade-control structures would be included within the bypass channel to achieve the necessary elevation change between Reach 2B and Reach 3. The grade control could be provided by structures such as sheet pile weirs or constructed rock riffles.
Rock riffles have benefits for native fish migration, but they present construction challenges in the sandy substrate of the Reach 2B and Reach 3 area. The flow over constructed rock riffles may reduce the disorienting effects on juveniles from rapidly
Mendota Pool Bypass and Reach 2B Improvements Project 3-56 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
changing hydraulics otherwise created at weir structures, and they are more favorable to sturgeon, which do not jump. Constructed rock riffles may be less favorable to predators which can hold in the quiescent pools below weir structures. However, placing rock in sandy substrate requires engineered foundation materials (layers of rock in gradually decreasing sizes) to prevent undermining the structure. Further analysis during design will determine which type of drop structure will be selected.
Sheet pile weirs would be constructed with capped and anchored sheet piles. Caps on the sheet piles would be used to avoid injuring fish and can be surfaced with natural materials (i.e., grouted rock) to emulate natural conditions which fish may be exposed to in non-manmade portions of the San Joaquin River.
Each drop structure would extend across the main channel and key into the overbanks a distance of approximately 50 feet to protect against flanking, resulting in a total structure width of about 420 feet.
Vegetated revetment would be included along both channel banks within the portion of the bypass containing the grade control structures to provide additional protection against flanking. It is assumed that the revetment would consist of buried riprap covered with topsoil, erosion control fabric, and native woody vegetation, so that fish would experience natural channel banks. Native woody vegetation directly upstream, downstream, and adjacent to the drop structures would provide shading and opportunities for juveniles to hide from predators.
3.5.6 Water Deliveries This Alternative includes the South Canal for making up to 2,500 cfs in water deliveries from the San Joaquin River to Mendota Pool. Water deliveries to the Pool would include diversion of Friant Dam releases that are meant to satisfy the Exchange Contract as well as diversion of San Joaquin River flood flows if there is demand in Mendota Pool.
3.5.7 Construction Considerations The total construction timeline for this Alternative is currently estimated to range approximately from 102 to 132 months (8.5 to 11 years); opportunities to shorten the overall schedule through construction efficiencies will be studied during the detailed design process.
Flow in the San Joaquin River, operations at the existing Mendota Dam, and operation of the existing Columbia Canal must be maintained during construction. It is anticipated that the majority of the Compact Bypass channel can be constructed without interruption to the San Joaquin River flow or the Columbia Canal.
The construction of the control structure across the existing river channel would require removable cofferdams in three phases to facilitate the construction without blocking the flow. If flow is present in the river during the construction period, flow will be diverted around the work area via a temporary diversion pipe or canal and fish passage will be provided. Cofferdams include two rows of braced sheet piling filled with dirt for stability and seepage control. The total height of the cofferdam is assumed to be 24 feet of which
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-57 – October 2012 San Joaquin River Restoration Program
12 feet would be above the channel bed. The control structures to be constructed on dry land (e.g., head of the South Canal) would not require cofferdams.
Stone slope protection (riprap) would be provided on the upstream and downstream slopes of the control structure embankment including some portions of the side slopes of the channel itself to prevent scouring. Riprap would be placed on bedding over geotextile fabric.
Construction of the fish screen and return/bypass fish pipes would take place in the dry using conventional construction methods and must be coordinated with construction of the water delivery canal. The exception to this is the outlet for the fish return pipes, which would require a cofferdam. All fish facility structures and pipes with surfaces exposed to fish require additional attention to surface-smoothness.
For construction of the control structures and fish passage facilities, a minimum flow must be maintained during construction; the amount or range of flows has not yet been identified. For construction at the bifurcation, it was assumed that construction would first be done away from the fish passage facility. A sheet pile cofferdam would be provided for the river control structure and/or the canal control structure and the water diverted away from the construction. Additional sheet piling would be provided to divert flows through the new bifurcation structure while the fish passage facility is constructed.
It was assumed that nuisance water will be in the San Mateo Avenue Crossing construction site and that installation of coffer dams would be required around portions of the work. Since a portion of the existing crossing is private (not a public road), it was assumed that access could be closed during construction. Construction would be timed (July 1 to November 1) so that the lesser Restoration Flows (5 to 195 cfs) can be routed around the structure during construction. At high flows water would flow over the structure, in addition to through the proposed culverts. To protect the structure during high flows, the proposed fill would be enclosed in concrete and cutoff walls and riprap would be included to prevent damage to the structure during over topping flows.
3.5.8 Summary The following tables summarize the levees, relocations, land acquisition, costs, benefits, and impacts associated with the Compact Alignment Bypass with Narrow Floodplain and South Canal Alternative based on design, field, and evaluation criteria data prepared for the Alternatives Evaluation. This data is preliminary for this TM and may be updated during the development of the Project EIS/R.
Mendota Pool Bypass and Reach 2B Improvements Project 3-58 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-3 Compact Bypass with Narrow Floodplain and South Canal Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 8.7 miles 7.1 miles Average Levee Height 5.8 feet 5.4 feet Fill Volume 345,200 cubic yards 269,700 cubic yards Relocations Electrical Distribution 43,500 feet Barn/Shed 1 Gas Transmission 10,000 feet Facility 1 Water Pipeline 31,000 feet Groundwater Well 26 Canal 32,500 feet Lift Pump 10 Culvert 1 Power Pole 144 Diversion 3 Dwelling 2 Land Acquisition1 Total 2,700 acres 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
Table 3-4 Compact Bypass with Narrow Floodplain and South Canal Costs Units of Categories Factors Criteria Quantity Measure Capital Improvement Costs dollars $487,640,000 Upfront Costs Land Costs dollars $29,690,000 Costs1 Subtotal dollars $517,330,000 Long-Term Costs O&M dollars/year $1,746,000 Time to Build Timeline Maximum Construction Time2 months 132 1 Costs were developed by DWR for the appraisal-level designs evaluated in Attachment A – Alternatives Evaluation. 2 Construction timeline does not include the time that would also be needed to complete the NEPA and CEQA documentation process, obtain permits, appraise and acquire land, and perform pre-construction surveys.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-59 – October 2012 San Joaquin River Restoration Program
Table 3-5 Compact Bypass with Narrow Floodplain and South Canal Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Wetlands acres 239.8 Marsh acres 43.9 Riparian wetland acres 140.5 Wet meadow acres 55.4 Other Waters acres 443.7 Sensitive Vegetation Alliances Alkali heath marsh acres 0.2 Arrow weed thickets acres 0.4 Black willow thickets acres 124.9 Blue elderberry stands acres 75.4 Special Status Button willow thickets acres 1.0 Vegetation and California bulrush marsh acres 16.9 Waters California rose briar patches acres 11.1 Creeping rye grass turfs acres 6.2 Fremont cottonwood forest acres 68.3 Oregon ash groves acres 6.9 Pale spike rush marshes acres 1.6 Red willow thicket acres 0.6 Existing Salt grass flats acres 1.4 Environmental Silver bush lupine scrub acres 2.0 Conditions Spinescale scrub acres 0.1 Tar plant fields acres 33.5 Yerba mansa meadows acres 0.8 Special status wildlife habitats Blunt-nosed leopard lizard acres 17.4 Fresno kangaroo rat acres 17.4 Giant garter snake acres 364.9 Greater sandhill crane acres 669.8 Special Status San Joaquin kit fox acres 201.6 Wildlife Swainson's hawk acres 441.4 Valley elderberry longhorn acres 75.4 beetle number of Valley elderberry longhorn elderberry 112 beetle shrubs number of listed Historic Properties 1 3 Cultural and properties Historical ranking: 1 (very Maximum Buried Deposits Resources low)-5 (very 4 Sensitivity high)
Mendota Pool Bypass and Reach 2B Improvements Project 3-60 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-5 Compact Bypass with Narrow Floodplain and South Canal Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Total Farmland in Production acres 1066.9 Alfalfa acres 46.5 Existing Almond acres 341.6 Socioeconomics Cotton acres 7.0 Crop Acreage and Economics Grapes acres 242.4 Conditions Other Row Crop acres 166.1 Palm acres 9.7 Pistachio acres 253.7 Primary production (<1.0 feet acres 477 Floodplain inundation at 2,500 cfs) Characteristics Rearing habitat (>1.0 feet acres 385 inundation at 2,500 cfs) Passage Artificial structures across number of Project Fish 20 Conditions for migratory path structures Habitat & Adult Chinook Maximum number of steps at number of Passage 43 Salmon structures jumps Conditions New fish screens along migratory number of Passage 3 path screens Conditions for Juvenile Chinook number of Potential predation sites artificial 21 Salmon structures 1 The number of listed properties is based on records from NRHP National Register of Historic Places, California Register of Historical Resources, Office for Historic Preservation Historic Property Directory, California State Historical Landmarks listing, California Inventory of Historic Resources, California Points of Historical Interest listing, the Caltrans State and Local Bridge Survey, and historical maps, including GLO Plat Maps. No previously recorded National Register or California Register eligible resources were identified in the records search.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-61 – October 2012 San Joaquin River Restoration Program
3.6 Compact Bypass with Wide Floodplain and Bifurcation Structure
The Compact Bypass with Wide Floodplain and Bifurcation Structure includes:
• Building levees capable of conveying flows up to 4,500 cfs with 3 feet of freeboard • Restoring floodplain habitat an average of approximately 4,200 feet wide to provide benefit to salmonids and other native fishes • Construction of a new channel and structures capable of conveying up to 4,500 cfs of Restoration Flows around the Mendota Pool • Construction of structures capable of conveying up to 2,500 cfs from Reach 2B to Mendota Pool • Providing upstream and downstream fish passage for adult and juvenile salmonids and other native fishes between Reach 2A and Reach 3 This Alternative would construct a channel between Reach 2B and Reach 3, the Compact Bypass Channel, in order to bypass the Mendota Pool. Restoration Flows would enter Reach 2B at the Chowchilla Bifurcation Structure, flow through Reach 2B, then downstream to Reach 3 via the Compact Bypass Channel. The existing Chowchilla Bifurcation Structure would continue to divert San Joaquin River flows into the Chowchilla Bypass during flood operations, and a fish passage facility and control structure modifications would be included at the San Joaquin River control structure at the Chowchilla Bypass to provide fish passage. A bifurcation structure would be built at the head of the Compact Bypass Channel to control diversions into Mendota Pool. Fish passage facilities and a fish screen would be built at the Compact Bypass bifurcation structure to provide passage around the structure and prevent fish being entrained in the diversion. A fish barrier would be built in Reach 3 to direct up-migrating fish into the Compact Bypass Channel. A new crossing would be built at the San Mateo Avenue crossing. These features are described in further detail in the sections below.
See Figure 3-8 and Figure 3-9 for a plan view of the Alternative’s features. In Section 3.7.7, Table 3-6, Table 3-7, and Table 3-8 list the quantities of levee construction, relocations, and land acquisition, costs, conditions, and features associated with this Alternative.
Mendota Pool Bypass and Reach 2B Improvements Project 3-62 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Figure 3-8 Plan View of Compact Bypass with Wide Floodplain and Bifurcation Structure
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-63 – October 2012 San Joaquin River Restoration Program
Figure 3-9 Inset Map of Compact Bypass with Wide Floodplain and Bifurcation Structure
Mendota Pool Bypass and Reach 2B Improvements Project 3-64 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.6.1 Fish Habitat and Passage The purpose of the floodplain would be to provide riparian and floodplain habitat and support the migration and seasonal rearing of salmonids and other native fishes in Reach 2B. The floodplain has an average width of approximately 4,200 feet and an inundated area of approximately 1,150 acres at 2,500 cfs.
This Alternative provides floodplain habitat resulting in approximately 650 acres of shallow water habitat for primary production as well as approximately 500 acres of habitat that supports direct rearing at 2,500 cfs. Approximately 55 percent of the floodplain in this Alternative would inundate less than 1 foot deep at 2,500 cfs. This Alternative also retains approximately 400 acres of shallow water habitat at flows up to 4,500 cfs. Figure 3-10 below presents conceptual inundation areas for primary production and rearing habitats as they vary by flow. Inundation acreages may change during the design process.
1200
1000
800
Depth of Inundation: 600
Acres Production <1ft 400 Rearing >1ft
200
0 1500 2000 2500 3000 3500 4000 4500 Flow (cfs)
Source: Tetra Tech 2012 Figure 3-10 Potential Inundation Acreage by Flow for Compact Bypass with Wide Floodplain and Bifurcation Structure
In the Compact Bypass channel, floodplain benches with an approximate average width of 300 feet on each side the main flow portion of the bypass channel are included (see Section 3.7.3 Compact Bypass Channel). Riparian and floodplain habitat would develop on the benches in the bypass channel to benefit migrating fish and promote a stable channel and sediment transport from Reach 2B to Reach 3.
This Alternative includes several facilities that fish would encounter or need to pass to migrate between Reach 3 and Reach 2B (from downstream to upstream):
• A fish barrier near the downstream end of the Compact Bypass
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-65 – October 2012 San Joaquin River Restoration Program
• Several (10 to 18) in-channel drop structures in the Compact Bypass • The San Mateo Avenue crossing (this crossing is included in all Alternatives) • Four fish screen return outlets from the Compact Bypass bifurcation structure fish screen • A bifurcation control structure at the upstream end of the Compact Bypass with fish passage facility • A fish screen near the upstream end of the Compact Bypass • Fish screens at Lone Willow Slough, Big and Little Bertha pumps, and other smaller diversions (these screens are included in all Alternatives) • The San Joaquin River control structure at the Chowchilla Bypass with a fish passage facility Each structure would be designed to perform according to the fish passage design criteria (see Section 3.4.1). In addition, the channel and floodplain incorporate riparian plantings to provide cover, woody material, and velocity variability, while the design footprint allows sufficient space to incorporate channel structure variability during detailed design, all of which may help to reduce stress and predation.
This Alternative includes a fish barrier at the downstream end of the bypass channel to keep fish from migrating into false migration pathways. Without the barrier, a false migration pathway up to the base of Mendota Dam would be available to fish in all years, and a false migration pathway into Mendota Pool and Fresno Slough (potentially into the King River system) would occur in about one in five years, when the boards are taken out of Mendota Dam to pass Pine Flat flood releases into Reach 3. However, with the barrier, which would be designed to accommodate flows up to 4,500 cfs, fish would not be able to migrate to Mendota Dam or enter Mendota Pool, but they would be guided into the bypass channel and Reach 2B.
3.6.2 Floodplain and Riparian Habitat This Alternative includes active riparian and floodplain habitat restoration. It is assumed that wetland communities (obligate, facultative-wet, and facultative species) would develop within the main channel, that a dense riparian scrubland would develop along the main river channel banks, and that bands of other habitat types (wetland, scrub, grassland, and forest) would develop at higher elevations along the channel corridor. The wetland, floodplain, and riparian areas would be planted following construction and then irrigated and managed as necessary during the establishment period. Invasive, non-native species would be removed from the Project area during or following construction, and the Project would include long-term management for invasives.
Several native vegetation alliances could be incorporated into the floodplain and habitat planting design. The grass-dominated vegetation alliances, which produce the maximum food benefits for salmon, could be more than twice as large as those that would develop with the narrow floodplain alternatives. All of the elevated areas of the meander loops could be maintained or restored to Saltgrass Flats. The adjacent existing wetland areas within the loops could be preserved or enhanced by additional wetland species plantings
Mendota Pool Bypass and Reach 2B Improvements Project 3-66 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
and removal of numerous invasive species. The lower lying portions of the reach could be planted with the Button Willow Thicket vegetation alliance. Because of the wide floodplain and the slowly moving water, the extent of this vegetation alliance could almost quadruple compared to what might develop in the narrow floodplain alternatives. The extent of Black Willow Thicket and California Mugwort Brush could also increase over what might develop in the narrow floodplain alternatives. Additional restoration work could focus on the re-establishment of the Riparian Bank Herbs, California Bulrush Marsh, Oregon Ash Groves, Creeping Rye Grasslands, and Fremont Cottonwood Forests. Because of the fast growth and its soft and brittle wood, the cottonwood is considered to be a good source of large woody debris and organic matter within the riverine channel. The riverside levee banks would be planted with native grass species such as those in the Creeping Rye Grassland alliance. Since creeping wild rye (Leymus triticoides) is a facultative wetland species that thrives in the upper parts of riparian areas, the extent of Creeping Rye Grassland could more than double compared to the narrow floodplain alternatives.
This Alternative would provide potential habitat for greater sandhill crane and Swainson’s hawk. The larger floodplains provide increasingly more potential habitat.
Figure 3-11 Typical distribution of vegetation alliances along a restored Reach 2B riparian bank section
Maintenance and Invasive Species Control Invasive, non-native species would be removed from the Project area during the installation, plant establishment and maintenance periods. Maintenance and invasives species control would be conducted as described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.2.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-67 – October 2012 San Joaquin River Restoration Program
Temporary Irrigation System and Water Supply Since all of the proposed plantings are wetland species or borderline wetland species, they would need regular overhead irrigation (typically April through October) during their establishment period (three to five years depending on rainfall conditions and the plants’ growth rates and vigor). The amount of water needed is estimated to be approximately 2.4 feet per acre per year. They would be irrigated with an extensive temporary surface mounted irrigation system that would provide water for the plants several times a week during the hot months of the year. The irrigation distribution piping would be installed aboveground and anchored to the ground with rebar soil staples so that it would not be damaged during high flows that would be regularly inundating the floodplain. The sprinkler heads would be installed on four-foot high, braced standpipes so that their irrigation stream would not be blocked or diverted by growing vegetation. The irrigation system would be disassembled and removed at the end of the establishment period.
The Program would pursue options for irrigation water supply, including groundwater wells or water pumped from the river with portable, skid-mounted, diesel- or gas- powered pumps and stored in tanks. Additionally, purchases from willing sellers may be required to withdraw water from the river or other nearby water sources (e.g., Mendota Pool). If water is pumped from the river, the amount of water diverted will be controlled so that river water temperatures do not increase and passage for salmonids is not impaired. The diversion from the river would also be screened to prevent entraining juvenile salmonids.
Existing Native Vegetation Protection Existing native vegetation protection would be conducted as described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.2.
Maintenance and Monitoring The key maintenance and monitoring activities include close monitoring of the installed plants for drought stress and overwatering, removal of competitive, invasive, non-native species, replacement of diseased and dead plants, irrigation system maintenance, and removal of trash and debris.
Close monitoring of the installed plants for both drought stress and overwatering would be performed because the proposed plants are native wetland species that can be quickly damaged by lack of irrigation.
For irrigation system maintenance, the system would be used intensively each year on a biweekly to daily basis during the hot part of the growing season. The landscape contractor would be required to regularly check the integrity of the system and make sure that none of the sprinkler heads are clogged or damaged.
Removal of trash and debris from the restoration areas on both sides of the river would be performed on an as-needed basis for the duration of the entire monitoring period.
Mendota Pool Bypass and Reach 2B Improvements Project 3-68 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.6.3 Compact Bypass Channel The Compact Bypass channel is the same as described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.3.
3.6.4 Structures The structures described below would be required to provide the operational flexibility to divert water to the Mendota Pool, provide fish passage, allow maintenance access to Mendota Dam, prevent fish entrainment and straying, and provide controlled elevation drop between Reach 2B and Reach 3.
San Joaquin River Control Structure at the Chowchilla Bypass Fish Passage Facility The San Joaquin River control structure at the Chowchilla Bypass would not be passable by up-migrating salmon and native fish for all flows and flow splits between the river and the Chowchilla Bypass. The undershot gates, sill across the downstream side of the structure, and trash rack on the upstream side contribute to upstream passage difficulties at high, low, and all flows, respectively. It was determined that a fish passage facility would be required for upmigrating salmon and other natives fish to swim into Reach 2A from Reach 2B under most conditions. The fish passage facility is the same as described for the South Canal in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
San Joaquin River Control Structure at the Chowchilla Bypass Modifications In addition to the passage facility, the San Joaquin River control structure at the Chowchilla Bypass would be modified to improve fish passage through the control structure itself or to improve operations of the passage facility. Fish passage through the modified river control structure may meet passage criteria only for certain flows, so the fish passage facility described above would still be required.
Improvements to the river control structure could include removing the trash racks, replacing one or more radial gates with over-shot gates (e.g. inflatable Obermeyer weir gates), notching or removal of the baffle wall or weir, removing the dragon’s teeth, and replacing or modifying the scour protection. Improvements would be designed to meet NMFS 2001 and NMFS 2008 passage criteria when flow conditions are amenable. Improvements would not affect the ability of the structure to divert flood water into the Chowchilla Bypass.
Replacement of San Mateo Avenue Crossing The existing river crossing at San Mateo Avenue would be replaced with a new culverted crossing. The crossing is the same as described in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5
Compact Bypass Bifurcation Structure A bifurcation structure would be constructed at the upstream end of the Compact Bypass. The bifurcation structure consists of two control structures: one across the path of Restoration Flows (Compact Bypass) and one across the path of water deliveries to Mendota Pool (San Joaquin River). Since this structure will be retaining the Pool, it
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-69 – October 2012 San Joaquin River Restoration Program
would likely be regulated by DSOD. The Compact Bypass bifurcation structure is the same as described for the South Canal in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Compact Bypass Fish Passage Facility The Compact Bypass control structure across the Restoration Flow path includes a fish passage facility. The fish passage facility would be necessary to provide passage during Pool deliveries and for Restoration Flows where passage conditions in the control structure may not be ideal. The design of the fish passage facility is the same as that presented for the South Canal in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Drive 10 ½ Crossing The Compact Alignment Bypass would cross existing Drive 10 ½, which provides access for the operations and maintenance of Mendota Dam. To continue the current level of access, the road would be rerouted along the bypass channel levees and cross the head of the bypass channel at the proposed Compact Bypass bifurcation structure. A road deck would also be provided over the fish passage facility adjacent to the bifurcation structure. The road would be designed for HS-20 loading (e.g., sufficient to allow transport of a 25- ton maintenance crane to Mendota Dam).
Compact Bypass Fish Screen A fish screen would be included adjacent to the head of the Compact Bypass where Pool deliveries would be diverted from the river. The fish screen would be necessary to keep or return out-migrating juvenile salmon to the path of Restoration Flows during Pool deliveries. The Compact Bypass fish screen is the same as described for the South Canal in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Mendota Dam Fish Barrier A fish exclusion barrier would be included in Reach 3 near the downstream end of the Compact Bypass to prevent adult fish from migrating beyond the bypass channel up to the base of Mendota Dam. The fish barrier is the same as described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Grade Control Structures A series of several (10 to 18), approximately 0.5-ft high grade-control structures would be included within the bypass channel to achieve the necessary elevation change between Reach 2B and Reach 3. The drop structures are the same as described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
3.6.5 Water Deliveries This Alternative includes a diversion at the head of the Compact Bypass for making up to 2,500 cfs in water deliveries from the San Joaquin River to Mendota Pool. This diversion would directly deliver water from the river to Mendota Pool without the need for a canal. Water deliveries to the Pool would include diversion of Friant Dam releases that are
Mendota Pool Bypass and Reach 2B Improvements Project 3-70 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
meant to satisfy the Exchange Contract as well as diversion of San Joaquin River flood flows if there is demand in Mendota Pool.
3.6.6 Construction Considerations The total construction timeline for this Alternative is currently estimated to range approximately from 106 to 157 months (9 to 13 years); opportunities to shorten the overall schedule through construction efficiencies will be studied during the detailed design process.
The construction considerations are the same as described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.7.
3.6.7 Summary The following tables summarize the levees, relocations, land acquisition, costs, benefits, and impacts associated with the Compact Alignment Bypass with Narrow Floodplain and Bifurcation Structure Alternative based on design, field, and evaluation criteria data prepared for the Alternatives Evaluation. This data is preliminary for this TM and may be updated during the development of the Project EIS/R.
Table 3-6 Compact Bypass with Wide Floodplain and Bifurcation Structure Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 8.1 miles 6.8 miles Average Levee Height 5.6 feet 4.7 feet Fill Volume 328,600 cubic yards 226,900 cubic yards Relocations Electrical Distribution 48,500 feet Barn/Shed 1 Gas Transmission 11,000 feet Facility 1 Water Pipeline 41,000 feet Groundwater Well 32 Canal 31,500 feet Lift Pump 10 Culvert 1 Power Pole 162 Diversion 3 Dwelling 2 Land Acquisition1 Total 2,900 acres 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-71 – October 2012 San Joaquin River Restoration Program
Table 3-7 Compact Bypass with Wide Floodplain and Bifurcation Structure Costs Units of Categories Factors Criteria Quantity Measure Capital Improvement Costs dollars $446,280,000 Upfront Costs Land Costs dollars $33,700,000 Costs1 Subtotal dollars $479,980,000 Long-Term Costs O&M dollars/year $1,241,000 Time to Build Timeline Maximum Construction Time2 months 157 1 Costs were developed by DWR for the appraisal-level designs evaluated in Attachment A – Alternatives Evaluation. 2 Construction timeline does not include the time that would also be needed to complete the NEPA and CEQA documentation process, obtain permits, appraise and acquire land, and perform pre-construction surveys.
Mendota Pool Bypass and Reach 2B Improvements Project 3-72 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-8 Compact Bypass with Wide Floodplain and Bifurcation Structure Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Wetlands acres 236.2 Marsh acres 40.3 Riparian wetland acres 143.7 Wet meadow acres 52.2 Other Waters acres 437.2 Sensitive Vegetation Alliances Alkali heath marsh acres 0.2 Arrow weed thickets acres 0.4 Black willow thickets acres 124.9 Blue elderberry stands acres 75.4 Special Status Button willow thickets acres 1.2 Vegetation and California bulrush marsh acres 12.8 Waters California rose briar patches acres 11.3 Creeping rye grass turfs acres 6.1 Fremont cottonwood forest acres 68.5 Oregon ash groves acres 7.0 Red willow thickets acres 0.6 Salt grass flats acres 1.4 Existing Environmental Silver bush lupine scrub acres 4.1 Conditions Spinescale scrub acres 0.1 Tar plant fields acres 34.9 Yerba mansa meadows acres 0.8 Special status wildlife habitats Blunt-nosed leopard lizard acres 15.4 Fresno kangaroo rat acres 15.4 Giant garter snake acres 348.3 Greater sandhill crane acres 635.3 Special Status San Joaquin kit fox acres 197.8 Wildlife Swainson's hawk acres 443.9 Valley elderberry longhorn acres 75.4 beetle number of Valley elderberry longhorn elderberry 113 beetle shrubs number of listed Historic Properties 1 3 Cultural and properties Historical ranking: 1 (very Maximum Buried Deposits Resources low)-5 (very 4 Sensitivity high)
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-73 – October 2012 San Joaquin River Restoration Program
Table 3-8 Compact Bypass with Wide Floodplain and Bifurcation Structure Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Total Farmland in Production acres 1302.1 Alfalfa acres 55.2 Existing Almond acres 512.0 Socioeconomics Cotton acres 7.0 Crop Acreage and Economics Grapes acres 175.6 Conditions Other Row Crop acres 102.5 Palm acres 9.7 Pistachio acres 440.1 Primary production (<1.0 feet acres 636 Floodplain inundation at 2,500 cfs) Characteristics Rearing habitat (>1.0 feet acres 527 inundation at 2,500 cfs) Passage Artificial structures across number of Project Fish 21 Conditions for migratory path structures Habitat & Adult Chinook Maximum number of steps at number of Passage 67 Salmon structures jumps Conditions New fish screens along migratory number of Passage 4 path screens Conditions for Juvenile Chinook number of Potential predation sites artificial 22 Salmon structures 1 The number of listed properties is based on records from NRHP National Register of Historic Places, California Register of Historical Resources, Office for Historic Preservation Historic Property Directory, California State Historical Landmarks listing, California Inventory of Historic Resources, California Points of Historical Interest listing, the Caltrans State and Local Bridge Survey, and historical maps, including GLO Plat Maps. No previously recorded National Register or California Register eligible resources were identified in the records search.
Mendota Pool Bypass and Reach 2B Improvements Project 3-74 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.7 Fresno Slough Dam with Narrow Floodplain and Short Canal
The Fresno Slough Dam with Narrow Floodplain and Short Canal includes:
• Building levees capable of conveying flows up to 4,500 cfs with 3 feet of freeboard • Restoring floodplain habitat an average of approximately 3,000 feet wide to provide benefit to salmonids and other native fishes • Construction of a dam capable of containing Mendota Pool within Fresno Slough so that 4,500 cfs of Restoration Flows can be conveyed around the Mendota Pool • Construction of the Short Canal and structures capable of conveying up to 2,500 cfs from Reach 2B to Mendota Pool • Providing upstream and downstream fish passage for adult and juvenile salmonids and other native fishes between Reach 2A and Reach 3 This Alternative would build a dam across Fresno Slough, the Fresno Slough Dam, to contain the Mendota Pool, and it would utilize the existing river channel in order to bypass the Mendota Pool. Restoration Flows would enter Reach 2B at the Chowchilla Bifurcation Structure, flow through Reach 2B, then downstream to Reach 3 over the sill at Mendota Dam. Mendota Pool would be contained south of the Fresno Slough Dam. The existing Chowchilla Bifurcation Structure would continue to divert San Joaquin River flows into the Chowchilla Bypass during flood operations, and a fish passage facility and control structure modifications would be included at the San Joaquin River control structure at the Chowchilla Bypass to provide fish passage. A canal to convey San Joaquin River water deliveries to Mendota Pool, the Short Canal, would be built adjacent to the Fresno Slough Dam. The Mendota Dam along with a control structure built at the head of the Short Canal would be used to control diversions into Mendota Pool through the Short Canal. Fish passage facilities at Mendota Dam and a fish screen on the Short Canal would be built to provide passage around Mendota Dam and prevent fish from being entrained in the diversion. A fish barrier would be built downstream of the Fresno Slough Dam to keep up-migrating fish in Reach 2B. A new crossing would be built at the San Mateo Avenue crossing. These features are described in further detail in the sections below.
See Figure 3-12 and Figure 3-13 for a plan view of the Alternative’s features. In Section 3.8.8, Table 3-9, Table 3-10, and Table 3-11 list the quantities of levee construction, relocations, and land acquisition, costs, conditions, and features associated with this Alternative.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-75 – October 2012 San Joaquin River Restoration Program
Figure 3-12 Plan View of Fresno Slough Dam with Narrow Floodplain and Short Canal
Mendota Pool Bypass and Reach 2B Improvements Project 3-76 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Figure 3-13 Inset Map of Fresno Slough Dam with Narrow Floodplain and Short Canal
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-77 – October 2012 San Joaquin River Restoration Program
3.7.1 Fish Habitat and Passage The purpose of the floodplain would be to provide riparian and floodplain habitat and support the migration and seasonal rearing of salmonids and other native fishes in Reach 2B. The floodplain has an average width of approximately 3,000 feet and an inundated area of approximately 750 acres at 2,500 cfs.
This Alternative provides floodplain habitat resulting in approximately 500 acres of shallow water habitat for primary production as well as approximately 250 acres of habitat that supports direct rearing at 2,500 cfs. For this Alternative, approximately 65 percent of the floodplain would inundate less than 1 foot deep at 2,500 cfs. This Alternative also retains approximately 200 acres of shallow water habitat at flows up to 4,500 cfs. Source: Tetra Tech 2012 Figure 3-14 below presents conceptual inundation areas for primary production and rearing habitats as they vary by flow. Inundation acreages may change during the design process.
1200
1000
800 Depth of Inundation:
600
Acres Production <1ft 400 Rearing >1ft
200
0 1500 2000 2500 3000 3500 4000 4500 Flow (cfs)
Source: Tetra Tech 2012 Figure 3-14 Potential Inundation Acreage by Flow for Fresno Slough Dam with Narrow Floodplain and Short Canal
This Alternative includes several facilities that fish would encounter or need to pass to migrate between Reach 3 and Reach 2B (from downstream to upstream):
• An estimated two to four in-channel drop structures below Mendota Dam • The sill of Mendota Dam (when boards are out) or a fish passage facility at Mendota Dam (when boards are in) • Four fish screen return outlets from the Short Canal fish screen • A fish barrier north of the Fresno Slough Dam • A fish screen near the upstream end of the Short Canal • The San Mateo Avenue crossing (this crossing is included in all Alternatives)
Mendota Pool Bypass and Reach 2B Improvements Project 3-78 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
• Fish screens at Lone Willow Slough, Big and Little Bertha pumps, and other smaller diversions (these screens are included in all Alternatives) • A bifurcation control structure at the Chowchilla Bypass with fish passage facility Each structure would be designed to perform according to the fish passage design criteria (see Section 3.4.1). In addition, the channel and floodplain incorporate riparian plantings to provide cover, woody material, and velocity variability, while the design footprint allows sufficient space to incorporate channel structure variability during detailed design, all of which may help to reduce stress and predation.
3.7.2 Floodplain and Riparian Habitat Floodplain and riparian habitat would be included in this Alternative as described for the Compact Bypass with Wide Floodplain and Bifurcation Structure Alternative in Section 3.7.2.
3.7.3 Short Canal The Short Canal would deliver up to 2,500 cfs in water deliveries from the San Joaquin River to Mendota Pool (see Section 3.8.6). The Short Canal could connect to the river either on the east or west side of the Fresno Slough Dam. Additionally, the west-side configuration could be combined with the Main Canal and Helm Ditch Relocations or be constructed independent of those relocations. The Short Canal would discharge into Fresno Slough approximately 0.8 river miles south of Mendota Dam.
Water deliveries would be controlled by a control structure at the north end of the Short Canal and Mendota Dam. The canal control structure would have a fish screen to prevent entrainment and Mendota Dam would be retrofitted with fish passage facilities. The control structures, fish screen, and fish passage facilities are discussed in Section 3.8.4.
The Short Canal would be concrete-lined with a trapezoidal cross-section. The Short Canal would have a top-width of approximately 70 feet, a total corridor width of approximately 180 feet (including levees and maintenance roads), and 2H to 1V side slopes on the canal banks and 3H to 1V side slopes on the levees. Levee heights would be based on a flow of 2,500 cfs and 3 feet of freeboard.
3.7.4 Structures The structures described below would be required to provide the operational flexibility to divert water to the Mendota Pool, provide fish passage, prevent fish entrainment and straying, and provide controlled elevation drop between Reach 2B and Reach 3.
Chowchilla Bifurcation Structure Fish Passage Facility The Chowchilla Bifurcation Structure fish passage facility is the same as that in the Compact Bypass with Wide Floodplain and Bifurcation Structure Alternative in Section 3.7.4.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-79 – October 2012 San Joaquin River Restoration Program
San Joaquin River control structure at the Chowchilla Bypass Modifications The San Joaquin River control structure at the Chowchilla Bypass modifications are the same as those in the Compact Bypass with Wide Floodplain and Bifurcation Structure Alternative in Section 3.7.4.
Replacement of San Mateo Avenue Crossing The existing river crossing at San Mateo Avenue would be replaced with a new culverted crossing. The crossing is the same as described in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5
Short Canal Control Structure A control structure would be constructed at the upstream end of the Short Canal. The control structure would be across the path of water deliveries to Mendota Pool. Since this structure will be retaining the Pool, it would likely be regulated by DSOD. The Short Canal control structure is the same as the control structure across the path of water deliveries described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Short Canal Fish Screen A fish screen would be included at the head of the Short Canal where Pool deliveries would be diverted from the river. The fish screen would be necessary to keep or return out-migrating juvenile salmon to the path of Restoration Flows during Pool deliveries. The Short Canal fish screen is the same as described for the South Canal in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Fresno Slough Dam The Fresno Slough Dam would be constructed approximately 0.5 miles south of the Mendota Dam, in the existing Fresno Slough. In addition, the dam structure would be located just south of the existing Mowry Bridge that crosses the Fresno Slough. The dam would serve to limit the extent of Mendota Pool so it no longer occupies portions of the San Joaquin River. This pool would feed the five existing irrigation canals (Main Canal, Helm Ditch, Columbia Canal, Outside Canal, and Main Lift Canal). A screened water diversion canal would enable water deliveries from the San Joaquin River to the Mendota Pool. Since inputs into the Mendota Pool would be screened, Fresno Slough Dam does not require provisions for fish passage. Since this structure will be retaining the Pool, it would likely be regulated by DSOD.
The dam structure would be designed to accommodate a maximum water elevation of 156 feet. This water elevation corresponds to a pool depth of 16 feet above the top of the concrete floor.
The Fresno Slough Dam would have a reinforced concrete spillway. The spillway would not require the support of piles. The spillway would include a concrete cutoff wall at the upstream end of the spillway to limit the hydrostatic uplift pressures and reduce the effects of scour. Baffle blocks and riprap would be included at the downstream end the concrete spillway to limit the effects of scour and erosion.
Mendota Pool Bypass and Reach 2B Improvements Project 3-80 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Directly adjacent to the upstream and downstream ends of the concrete dam structure, a total of four concrete retaining walls form the walls of the spillway, and retain the sides of the earthen embankment portion of the dam. The spillway structure would be comprised of multiple gates, which serve to control the flow of water from the Mendota Pool to the San Joaquin River.
Over the dam, a concrete roadway, concrete maintenance platform, and a hoist operation platform span the full width of the structure. A series of vertical stoplog slots would be included in the concrete abutment walls. The stoplog slots allow the placement of stoplogs directly upstream of the gates, to facilitate local dewatering of the gates for maintenance operations.
Some excavation of existing channel sediments upstream of the dam will be required to improve flow conditions through the dam during Kings River floods.
Fresno Slough Dam Fish Barrier A fish exclusion barrier would be included north of the Fresno Slough Dam to prevent adult fish from migrating into Fresno Slough during Kings River flood releases through the Fresno Slough Dam. Levees would be constructed to delineate a channel between the Fresno Slough Dam and the fish barrier, and sediments in the San Joaquin River would be excavated to allow proper structure placement and acceptable sweeping velocities.
The design of the fish barrier is the same as the Mendota Dam fish barrier described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Mendota Dam Modifications This Alternative includes using the San Joaquin River channel as a means of bypassing Mendota Pool. Since the Mendota Dam crosses the San Joaquin River, the structure will need to be modified to provide run-of-the-river conditions during Restoration Flows. The concrete portions of structure of Mendota Dam would remain in place, and the flash boards currently used to close the bays and back up water would be removed during non- water delivery operations using the Short Canal. The sill of the dam may be notched in one or more bays to improve fish passage conditions, and the notch would be designed to accommodate flash boards similar to the current bays. When the Short Canal is in operation, the flash boards would be placed in the notch(es) and bays to back up water for water deliveries.
Mendota Dam Fish Passage Facilities Fish passage facilities are provided at Mendota Dam for two conditions: when the boards are out and when the boards are in. Most of the time, the flash boards at Mendota Dam will be out, and Restoration Flows will pass unimpeded over the sill at Mendota Dam. When water deliveries from the river to Mendota Pool are occurring, the flash boards at Mendota Dam will be installed to create an impoundment. Due to the variation in conditions, different fish passage facilities are required for each condition.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-81 – October 2012 San Joaquin River Restoration Program
Boards-Out Conditions (no water deliveries occurring) Passage for boards-out conditions could be accomplished with either grade-control structures, dam notching, a fish passage facility, or a combination of these.
A series of approximately 0.5-feet high grade control structures could be installed downstream of Mendota Dam to increase the water surface elevation during low flows of around 100 cfs to allow fish passage over the sill when the boards are out at Mendota Dam. The structures would be located several hundred feet apart. Each structure would raise the water surface incrementally on the downstream side of the dam so that salmonids would be able to migrate over the sill. Other aspects of the grade control structures are the same as those described for those in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
The sill of the dam could also be notched to provide suitable low flow passage conditions when the boards are out. Notching the dam would involve removing portions of the existing concrete sill and potentially reinforcing the remaining concrete. The notch(es) would be designed to accommodate flash boards so that water delivery operations could occur. Notching could be utilized in combination with the grade control structures to reduce the overall number of structures needed to incrementally raise the water surface on the downstream side of the dam.
Alternatively, a fish passage facility could be installed at Mendota Dam to provide passage when the boards are out. The boards-out fish passage facility could be combined with the boards-in fish passage facility (described below) by including multiple entrances and exits on the facility. Otherwise, an independent fish passage facility for boards-out conditions could be constructed. The design of the boards-out fish passage facility is the same as described for the South Canal fish passage facility in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Boards-In Conditions (during water deliveries) For the Short Canal to operate, the boards at Mendota Dam would be replaced to raise the water surface in the river and back up water into the Mendota Pool. A proposed fish passage facility enables fish to pass over Mendota Dam when the boards are in. The passage facility transitions from the minimum San Joaquin River water surface elevation in Reach 3 (occurring during low flow/base flow conditions) to the normal pool water surface elevation above Mendota Dam. The boards-in fish passage facility could be combined with the boards-out fish passage facility (described above) by including multiple entrances and exits on the facility. Otherwise, an independent fish passage facility for boards-in conditions would be constructed. The design of the boards-in fish passage facility is the same as described for the South Canal fish passage facility in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Main Canal and Helm Ditch Relocations The Fresno Slough Dam requires the headworks of the Central California Irrigation District’s (CCID) Main Canal and Helm Ditch to be reconfigured to divert water from the upstream (south) side of the Fresno Slough Dam. This would allow the District to
Mendota Pool Bypass and Reach 2B Improvements Project 3-82 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
continue to receive their water supply from the Delta Mendota Canal and flows from the Fresno Slough without requiring screening of those diversions.
To provide water to the CCID’s Main Canal and Helm Ditch, an inlet canal is proposed that would take water from the upstream side of the proposed Fresno Slough Dam, run north adjacent to the west side of the San Joaquin River, and connect to the Main Canal and Helm Ditch just west of their current intakes. This canal would be capable of conveying the full flow of both the Main Canal and the Helm Ditch combined (1550 cfs).
The inlet canal would be designed to pass the design flow at anticipated low water levels in the Pool, but it would still provide 2 feet of freeboard at the anticipated high water level. The water elevation in the inlet canal would essentially float with the Mendota Pool. A bridge over the inlet canal would be required to maintain access to Mowry Bridge and the future Fresno Slough Dam. Currently, there is a 20-inch drinking water pipeline for the City of Mendota that crosses the Mowry Bridge. This pipeline would need to be modified so that it crosses the proposed inlet canal on the proposed bridge.
The inlet canal would be concrete lined in locations where erosion is likely to be a concern (i.e., at bends and transitions), and riprap would be placed at the transition from the Pool to the inlet channel.
A concrete control structure would control the water from the inlet canal. It would function to control flows to both the Main Canal and the Helm Ditch. Controlling the flow to the Main Canal would be accomplished with control gates Upstream of the gates on the eastern wall, a pipeline would deliver water to the relocated head of the Helm Ditch. The concrete pipe, equipped with a canal gate, would serve to control the flow rate as well as shutoff point. It is assumed that existing headworks and telemetry for both the Main Canal and Helm Ditch would be removed from the site, and new telemetry would be installed.
The upstream side of the Main Canal structure would have a cutoff wall to prevent undermining the structure. Downstream of the control structure, the Main Canal would transition both vertically and horizontally into the existing Main Canal alignment and cross-section. The extension of Helm Ditch would be designed to match the cross-section of the existing Helm Ditch downstream.
3.7.5 Removal of River Sediments This Alternative would make use of the existing river channel from the Chowchilla Bifurcation Structure (approximately RM 216) down to Mendota Dam (approximately RM 204.6) in order to convey Restoration Flows. Since a portion of this river segment is currently impounded by Mendota Dam, sediment has filled in the pre-Mendota Dam channel. This Alternative assumes that the sediment would be excavated from portions of the former Pool impoundment area to establish a new equilibrium channel slope. The cost of removing sediment over an estimated channel cross-section, equilibrium slope, and length is included in the cost of this Alternative. If sediments meet on-site disposal criteria, they may be used to backfill soil borrow areas or to grade low areas on the floodplain.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-83 – October 2012 San Joaquin River Restoration Program
3.7.6 Water Deliveries This Alternative includes the Short Canal for making up to 2,500 cfs in water deliveries from the San Joaquin River to Mendota Pool. Water deliveries to the Pool would include diversion of Friant Dam releases that are meant to satisfy the Exchange Contract as well as diversion of San Joaquin River flood flows if there is demand in Mendota Pool
When water deliveries need to occur, the normal pool elevation in Mendota Pool may be higher than the water surface in the river at Fresno Slough Dam. In order for the Short Canal to be able to deliver water into Mendota Pool, the flash boards of Mendota Dam would be installed, and the water surface in the river would be raised until water could flow from the river south into Mendota Pool via the Short Canal. A fish screen would be included at the Short Canal, and fish passage facilities would be included at Mendota Dam when the boards are in and the diversion is operating.
3.7.7 Construction Considerations The total construction timeline for this Alternative is currently estimated to range approximately from 91 to 133 months (7.5 to 11 years); opportunities to shorten the overall schedule through construction efficiencies will be studied during the detailed design process.
Soil improvements to mitigate for possible liquefiable soils may be required.
Construction of the Fresno Slough Dam must not interrupt water deliveries. To accomplish this, the construction of the dam would require removable cofferdams in three phases to facilitate the construction without blocking the flow. If flow is present in the slough during the construction period, flow will be diverted around the work area via a temporary diversion pipe or canal and fish passage will be provided.
Construction of the fish screen and return/bypass fish pipes would take place in the dry using conventional construction methods and must be coordinated with construction of the water delivery canal. The exception to this is the outlet for the fish return pipes, which would require a cofferdam. All fish facility structures and pipes with surfaces exposed to fish require additional attention to surface-smoothness.
For construction of the control structures and fish passage facilities, a minimum flow must be maintained during construction; the amount or range of flows has not yet been identified. For construction at the bifurcation, it was assumed that construction would first be done away from the fish passage facility. A sheet pile cofferdam would be provided for the river control structure and/or the canal control structure and the water diverted away from the construction. Additional sheet piling would be provided to divert flows through the new bifurcation structure while the fish passage facility is constructed.
3.7.8 Summary The following tables summarize the levees, relocations, land acquisition, costs, benefits, and impacts associated with the Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative based on design, field, and evaluation criteria data prepared for the
Mendota Pool Bypass and Reach 2B Improvements Project 3-84 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Alternatives Evaluation. This data is preliminary for this TM and may be updated during the development of the Project EIS/R.
Table 3-9 Fresno Slough Dam with Narrow Floodplain and Short Canal Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 7.7 miles 6.9 miles Average Levee Height 5.6 feet 5.2 feet Fill Volume 317,500 cubic yards 224,500 cubic yards Relocations Electrical Distribution 48,000 feet Barn/Shed 1 Gas Transmission 9,000 feet Facility 1 Water Pipeline 33,000 feet Groundwater Well 25 Canal 32,500 feet Lift Pump 10 Culvert 1 Power Pole 166 Diversion 3 Dwelling 2 Land Acquisition1 Total 2,450 acres 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
Table 3-10 Fresno Slough Dam with Narrow Floodplain and Short Canal Costs Units of Categories Factors Criteria Quantity Measure Capital Improvement Costs dollars $465,470,000 Upfront Costs Land Costs dollars $24,700,000 Costs1 Subtotal dollars $490,170,000 Long-Term Costs O&M dollars/year $1,100,000 Time to Build Timeline Maximum Construction Time2 months 133 1 Costs were developed by DWR for the appraisal-level designs evaluated in Attachment A – Alternatives Evaluation. 2 Construction timeline does not include the time that would also be needed to complete the NEPA and CEQA documentation process, obtain permits, appraise and acquire land, and perform pre-construction surveys.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-85 – October 2012 San Joaquin River Restoration Program
Table 3-11 Fresno Slough Dam with Narrow Floodplain and Short Canal Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Wetlands acres 215.8 Marsh acres 61.7 Riparian wetland acres 101.9 Wet meadow acres 52.2 Other Waters acres 469.9 Sensitive Vegetation Alliances Alkali heath marsh acres 0.7 Arrow weed thickets acres 0.4 Black willow thickets acres 120.0 Blue elderberry stands acres 75.4 Special Status Button willow thickets acres 1.6 Vegetation and California bulrush marsh acres 24.8 Waters California rose briar patches acres 13.0 Creeping rye grass turfs acres 6.1 Fremont cottonwood forest acres 45.3 Oregon ash groves acres 7.0 Red willow thickets acres 0.6 Salt grass flats acres 1.7 Existing Silver bush lupine scrub acres 4.1 Environmental Spinescale scrub acres 0.7 Conditions Tar plant fields acres 35.4 Valley oak woodland Acres 0.2 Yerba mansa meadows acres 0.8 Special status wildlife habitats Blunt-nosed leopard lizard acres 15.4 Fresno kangaroo rat acres 15.4 Giant garter snake acres 436.0 Greater sandhill crane acres 539.9 Special Status San Joaquin kit fox acres 185.6 Wildlife Swainson's hawk acres 366.3 Valley elderberry longhorn acres 75.4 beetle number of Valley elderberry longhorn elderberry 113 beetle shrubs number of listed Historic Properties 1 4 Cultural and properties Historical ranking: 1 (very Maximum Buried Deposits Resources low)-5 (very 4 Sensitivity high)
Mendota Pool Bypass and Reach 2B Improvements Project 3-86 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-11 Fresno Slough Dam with Narrow Floodplain and Short Canal Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Total Farmland in Production acres 795.7 Alfalfa acres 21.5 Existing Almond acres 339.7 Socioeconomics Cotton acres 13.4 Crop Acreage and Economics Grapes acres 92.8 Conditions Other Row Crop acres 65.0 Palm acres 9.7 Pistachio acres 253.6 Primary production (<1.0 feet acres 528 Floodplain inundation at 2,500 cfs) Characteristics Rearing habitat (>1.0 feet acres 235 inundation at 2,500 cfs) Passage Artificial structures across number of Project Fish 13 Conditions for migratory path structures Habitat & Adult Chinook Maximum number of steps at number of Passage 59 Salmon structures jumps Conditions New fish screens along migratory number of Passage 3 path screens Conditions for Juvenile Chinook number of Potential predation sites artificial 14 Salmon structures 1 The number of listed properties is based on records from NRHP National Register of Historic Places, California Register of Historical Resources, Office for Historic Preservation Historic Property Directory, California State Historical Landmarks listing, California Inventory of Historic Resources, California Points of Historical Interest listing, the Caltrans State and Local Bridge Survey, and historical maps, including GLO Plat Maps. No previously recorded National Register or California Register eligible resources were identified in the records search.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-87 – October 2012 San Joaquin River Restoration Program
3.8 Fresno Slough Dam with Wide Floodplain and North Canal
The Fresno Slough Dam with Wide Floodplain and North Canal includes:
• Building levees capable of conveying flows up to 4,500 cfs with 3 feet of freeboard • Restoring floodplain habitat an average of approximately 4,200 feet wide to provide benefit to salmonids and other native fishes • Construction of a dam capable of containing Mendota Pool within Fresno Slough so that 4,500 cfs of Restoration Flows can be conveyed around the Mendota Pool • Construction of the North Canal and structures capable of conveying up to 2,500 cfs from Reach 2B to Mendota Pool • Providing upstream and downstream fish passage for adult and juvenile salmonids and other native fishes between Reach 2A and Reach 3 This Alternative would build a dam across Fresno Slough, the Fresno Slough Dam, to contain the Mendota Pool, and it would utilize the existing river channel in order to bypass the Mendota Pool. Restoration Flows would enter Reach 2B, flow through the reach, then downstream to Reach 3 over the sill at Mendota Dam. Mendota Pool would be contained south of the Fresno Slough Dam. A canal to convey San Joaquin River water deliveries to Mendota Pool, the North Canal, would be built. The San Joaquin River control structure at the Chowchilla Bypass would be removed, and a bifurcation structure would be built at the head of the North Canal to control flood diversions into the Chowchilla Bypass and water delivery diversions into Mendota Pool. Fish passage facilities and a fish screen would be built at the North Canal bifurcation structure to provide passage around the structure and prevent fish being entrained in the diversion. A fish barrier would be built downstream of the Fresno Slough Dam to keep up-migrating fish in Reach 2B. A new crossing would be built at the San Mateo Avenue crossing. These features are described in further detail in the sections below.
See Figure 3-15 and Figure 3-16 for a plan view of the Alternative’s features. In Section 3.9.8, Table 3-12, Table 3-13, and Table 3-14 list the quantities of levee construction, relocations, and land acquisition, costs, conditions, and features associated with this Alternative.
Mendota Pool Bypass and Reach 2B Improvements Project 3-88 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Figure 3-15 Plan View of Fresno Slough Dam with Wide Floodplain and North Canal
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-89 – October 2012 San Joaquin River Restoration Program
Figure 3-16 Inset Map of Fresno Slough Dam with Wide Floodplain and North Canal
Mendota Pool Bypass and Reach 2B Improvements Project 3-90 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
3.8.1 Fish Habitat and Passage The purpose of the floodplain would be to provide riparian and floodplain habitat and support the migration and seasonal rearing of salmonids and other native fishes in Reach 2B. The floodplain has an average width of approximately 4,200 feet and an inundated area of approximately 1,050 acres at 2,500 cfs.
This Alternative provides floodplain habitat resulting in approximately 750 acres of shallow water habitat for primary production as well as approximately 300 acres of habitat that supports direct rearing at 2,500 cfs. Approximately 70 percent of the floodplain in this Alternative would inundate less than 1 foot deep at 2,500 cfs. This Alternative also retains approximately 500 acres of shallow water habitat at flows up to 4,500 cfs. Source: Tetra Tech 2012 Figure 3-17 below presents conceptual inundation areas for primary production and rearing habitats as they vary by flow. Inundation acreages may change during the design process.
1200
1000
800
Depth of Inundation: 600
Acres Production <1ft 400 Rearing >1ft
200
0 1500 2000 2500 3000 3500 4000 4500 Flow (cfs)
Source: Tetra Tech 2012 Figure 3-17 Potential Inundation Acreage by Flow for Fresno Slough Dam with Wide Floodplain and North Canal
This Alternative includes several facilities that fish would encounter or need to pass to migrate between Reach 3 and Reach 2B (from downstream to upstream):
• An estimated two to four in-channel drop structures below Mendota Dam • The sill of Mendota Dam • A fish barrier north of the Fresno Slough Dam • The San Mateo Avenue crossing (this crossing is included in all Alternatives) • Four fish screen return outlets from the North Canal fish screen • A bifurcation control structure at the North Canal with fish passage facility • A fish screen near the upstream end of the North Canal
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-91 – October 2012 San Joaquin River Restoration Program
• Fish screens at Lone Willow Slough, Big and Little Bertha pumps, and other smaller diversions (these screens are included in all Alternatives) Each structure represents a potential stressor for adult salmon and potential predation site for juvenile salmon. However, each structure would be designed to perform according to the fish passage design criteria (see Section 3.4.1). In addition, the channel and floodplain incorporate riparian plantings to provide cover, woody material, and velocity variability, while the design footprint allows sufficient space to incorporate channel structure variability during detailed design, all of which may help to reduce stress and predation.
3.8.2 Floodplain and Riparian Habitat Floodplain and riparian habitat restoration actions similar to those described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.2.would be included in this Alternative.
3.8.3 North Canal The North Canal would deliver up to 2,500 cfs in water deliveries from the San Joaquin River to Mendota Pool (see Section 3.9.6). The North Canal could connect to the river at various locations, ideally on a straight section of the river or on the outside of bend. Three optional locations for the junction with the San Joaquin River are shown in Figure 3-4 at approximately RM 209.8, RM 213.4, and RM 214.2. The North Canal would discharge into Fresno Slough approximately 1.8 river miles south of Mendota Dam.
Other aspects of the North Canal are the same as those described for the South Canal in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.4.
3.8.4 Structures The structures described below would be required to provide the operational flexibility to divert water to the Mendota Pool, provide fish passage, prevent fish entrainment and straying, and provide controlled elevation drop between Reach 2B and Reach 3.
San Joaquin River control structure at the Chowchilla Bypass Removal The Chowchilla Bifurcation Structure consists of two control structures: one at the head of the Chowchilla Bypass and one across the San Joaquin River at RM 216. With the inclusion of a bifurcation structure at the head of the North Canal, a new control structure would be built across the San Joaquin River at the head of the canal. The new control structure would alleviate the need for the San Joaquin River control structure at the Chowchilla Bypass because all diversions into the Chowchilla Bypass could be controlled from the new control structure at the head of the North Canal. As part of this Alternative, the San Joaquin River control structure at the Chowchilla Bypass would be demolished.
North Canal Bifurcation Structure A bifurcation structure would be constructed at the upstream end of the North Canal. The bifurcation structure consists of two control structures: one across the path of Restoration Flows (San Joaquin River) and one across the path of water deliveries to Mendota Pool
Mendota Pool Bypass and Reach 2B Improvements Project 3-92 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
(North Canal). The North Canal bifurcation structure is the same as described for the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
North Canal Fish Passage Facility The North Canal bifurcation structure would include a fish passage facility on the side of the control structure across the Restoration Flow path. The fish passage facility would be necessary to provide passage during Pool deliveries and for Restoration Flows where passage conditions through the control structure may not be ideal. The design of the fish passage facility is the same as that presented for the South Canal fish passage facility in Section 3.6.5.
North Canal Fish Screen A fish screen would be included at the head of the North Canal where Pool deliveries would be diverted from the river. The fish screen would be necessary to keep or return out-migrating juvenile salmon to the path of Restoration Flows during Pool deliveries. The North Canal fish screen is the same as described for the South Canal in the Compact Bypass with Narrow Floodplain and South Canal Alternative in Section 3.6.5.
Removal of San Mateo Avenue Crossing The San Mateo Avenue crossing is an existing river crossing located within a public right-of-way in Madera County and on private land in Fresno County at approximately RM 211.8. The crossing transitions from public right-of-way to private land at the center of the river. The crossing consists of a low flow or dip crossing with a single culvert. As part of this Alternative, the culvert and road embankments would be demolished, and no river crossing would be provided at this location.
Fresno Slough Dam The Fresno Slough Dam is the same as that described in the Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative in Section 3.8.4.
Fresno Slough Dam Fish Barrier The Fresno Slough Dam fish barrier is the same as that described in the Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative in Section 3.8.4.
Mendota Dam Fish Passage Facilities The Mendota Dam fish passage facilities are the same as described for the boards-out condition in the Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative in Section 3.8.4
Main Canal and Helm Ditch Relocations The Main Canal and Helm Ditch relocations are the same as described in the Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative in Section 3.8.4.
3.8.5 Removal of River Sediments The removal of river sediment is the same as described in the Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative in Section 3.8.5
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-93 – October 2012 San Joaquin River Restoration Program
3.8.6 Water Deliveries This Alternative includes the North Canal for making up to 2,500 cfs in water deliveries from the San Joaquin River to Mendota Pool. Water deliveries to the Pool would include diversion of Friant Dam releases that are meant to satisfy the Exchange Contract as well as diversion of San Joaquin River flood flows if there is demand in Mendota Pool.
3.8.7 Construction Considerations The total construction timeline for this Alternative is currently estimated to range approximately from 97 to 158 months (8 to 13 years); opportunities to shorten the overall schedule through construction efficiencies will be studied during the detailed design process.
The construction considerations are the same as described for the Fresno Slough Dam with Narrow Floodplain and Short Canal Alternative in Section 3.8.7.
3.8.8 Summary The following tables summarize the levees, relocations, land acquisition, costs, benefits, and impacts associated with the Fresno Slough Dam with Wide Floodplain and North Canal Alternative based on design, field, and evaluation criteria data prepared for the Alternatives Evaluation. This data is preliminary for this TM and may be updated during the development of the Project EIS/R.
Table 3-12 Fresno Slough Dam with Wide Floodplain and North Canal Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 7.2 miles 6.6 miles Average Levee Height 5.2 feet 4.2 feet Fill Volume 272,000 cubic yards 188,250 cubic yards Relocations Electrical Distribution 68,000 feet Barn/Shed 1 Gas Transmission 11,500 feet Facility 1 Water Pipeline 50,000 feet Groundwater Well 32 Canal 56,000 feet Lift Pump 10 Culvert 1 Power Pole 239 Diversion 3 Dwelling 2 Land Acquisition1 Total 3,300 acres 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
Mendota Pool Bypass and Reach 2B Improvements Project 3-94 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-13 Fresno Slough Dam with Wide Floodplain and North Canal Costs Units of Categories Factors Criteria Quantity Measure Capital Improvement Costs dollars $469,500,000 Upfront Costs Land Costs dollars $35,890,000 Costs1 Subtotal dollars $505,390,000 Long-Term Costs O&M dollars/year $1,387,000 Time to Build Timeline Maximum Construction Time2 months 158 1 Costs were developed by DWR for the appraisal-level designs evaluated in Attachment A – Alternatives Evaluation. 2 Construction timeline does not include the time that would also be needed to complete the NEPA and CEQA documentation process, obtain permits, appraise and acquire land, and perform pre-construction surveys.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-95 – October 2012 San Joaquin River Restoration Program
Table 3-14 Fresno Slough Dam with Wide Floodplain and North Canal Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Wetlands acres 218.7 Marsh acres 60.5 Riparian wetland acres 106.0 Wet meadow acres 52.2 Other Waters acres 476.7 Sensitive Vegetation Alliances Alkali heath marsh acres 0.7 Arrow weed thickets acres 0.4 Black willow thickets acres 119.8 Blue elderberry stands acres 75.4 Special Status Button willow thickets acres 1.4 Vegetation and California bulrush marsh acres 23.6 Waters California rose briar patches acres 12.5 Creeping rye grass turfs acres 6.1 Fremont cottonwood forest acres 52.5 Oregon ash groves acres 6.9 Red willow thickets acres 0.6 Salt grass flats acres 1.7 Existing Silver bush lupine scrub acres 2.0 Environmental Spinescale scrub acres 0.7 Conditions Tar plant fields acres 33.9 Valley oak woodland Acres 0.2 Yerba mansa meadows acres 0.8 Special status wildlife habitats Blunt-nosed leopard lizard acres 15.2 Fresno kangaroo rat acres 15.2 Giant garter snake acres 438.9 Greater sandhill crane acres 740.4 Special Status San Joaquin kit fox acres 179.4 Wildlife Swainson's hawk acres 393.5 Valley elderberry longhorn acres 75.4 beetle number of Valley elderberry longhorn elderberry 112 beetle shrubs number of listed Historic Properties 1 4 Cultural and properties Historical ranking: 1 (very Maximum Buried Deposits Resources low)-5 (very 4 Sensitivity high)
Mendota Pool Bypass and Reach 2B Improvements Project 3-96 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-14 Fresno Slough Dam with Wide Floodplain and North Canal Conditions and Features within the Project Boundary Units of Categories Factors Criteria Quantity Measure Total Farmland in Production acres 1620.0 Alfalfa acres 48.3 Existing Almond acres 557.7 Socioeconomics Cotton acres 13.4 Crop Acreage and Economics Grapes acres 271.3 Conditions Other Row Crop acres 200.9 Palm acres 9.7 Pistachio acres 518.6 Primary production (<1.0 feet acres 741 Floodplain inundation at 2,500 cfs) Characteristics Rearing habitat (>1.0 feet acres 319 inundation at 2,500 cfs) Passage Artificial structures across number of Project Fish 13 Conditions for migratory path structures Habitat & Adult Chinook Maximum number of steps at number of Passage 36 Salmon structures jumps Conditions New fish screens along migratory number of Passage 3 path screens Conditions for Juvenile Chinook number of Potential predation sites artificial 14 Salmon structures 1 The number of listed properties is based on records from NRHP National Register of Historic Places, California Register of Historical Resources, Office for Historic Preservation Historic Property Directory, California State Historical Landmarks listing, California Inventory of Historic Resources, California Points of Historical Interest listing, the Caltrans State and Local Bridge Survey, and historical maps, including GLO Plat Maps. No previously recorded National Register or California Register eligible resources were identified in the records search.
3.9 Alternatives Comparison Tables
The tables below combine the summary tables from Sections 0, 3.7.7, 3.8.8, and 3.9.8 in order to allow easy cross-comparison of the Alternatives.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-97 – October 2012 San Joaquin River Restoration Program
Table 3-15 Levees, Relocations, and Land Acquisition Levees Compact Bypass with Compact Bypass with Fresno Slough Dam with Fresno Slough Dam with Narrow Floodplain and Wide Floodplain and Narrow Floodplain and Wide Floodplain and South Canal Bifurcation Structure Short Canal North Canal Left Levee Length 8.7 miles 8.1 miles 7.7 miles 7.2 miles Left Average Levee Height 5.8 feet 5.6 feet 5.6 feet 5.2 feet Left Fill Volume 345,200 cubic yards 328,600 cubic yards 317,500 cubic yards 272,000 cubic yards Right Levee Length 7.1 miles 6.8 miles 6.9 miles 6.6 miles Right Average Levee Height 5.4 feet 4.7 feet 5.2 feet 4.2 feet Right Fill Volume 269,700 cubic yards 226,900 cubic yards 224,500 cubic yards 188,250 cubic yards Relocations Electrical Distribution 43,500 feet 48,500 feet 48,000 feet 68,000 feet Gas Transmission 10,000 feet 11,000 feet 9,000 feet 11,500 feet Water Pipeline 31,000 feet 41,000 feet 33,000 feet 50,000 feet Canal 32,500 feet 31,500 feet 32,500 feet 56,000 feet Culvert 1 1 1 1 Diversion 3 3 3 3 Barn/Shed 1 1 1 1 Facility 1 1 1 1 Groundwater Well 26 32 25 32 Lift Pump 10 10 10 10 Power Pole 144 162 166 239 Dwelling 2 2 2 2 Land Acquisition1 Total 2,700 acres 2,900 acres 2,450 acres 3,300 acres 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
Mendota Pool Bypass and Reach 2B Improvements Project 3-98 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-16 Costs Compact Fresno Fresno Compact Bypass with Slough Dam Slough Dam Bypass with Wide with Narrow with Wide Units of Narrow Categories Factors Criteria Floodplain Floodplain Floodplain Measure Floodplain and and Short and North and South Bifurcation Canal Canal Canal Structure Capital Improvement Costs dollars $487,640,000 $446,280,000 $465,470,000 $469,500,000 Upfront Costs Land Costs dollars $29,690,000 $33,700,000 $24,700,000 $35,890,000 Costs1 Subtotal dollars $517,330,000 $479,980,000 $490,170,000 $505,390,000 Long-Term Costs O&M dollars/year $1,746,000 $1,241,000 $1,100,000 $1,387,000 Time to Build Timeline Maximum Construction Time2 months 132 157 133 158 1 Costs were developed by DWR for the appraisal-level designs evaluated in Attachment A – Alternatives Evaluation. 2 Construction timeline does not include the time that would also be needed to complete the NEPA and CEQA documentation process, obtain permits, appraise and acquire land, and perform pre-construction surveys.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-99 – October 2012 San Joaquin River Restoration Program
Table 3-17 Conditions and Features within the Project Boundaries Compact Fresno Fresno Compact Bypass with Slough Dam Slough Dam Bypass with Wide with Narrow with Wide Units of Narrow Categories Factors Criteria Floodplain Floodplain Floodplain Measure Floodplain and and Short and North and South Bifurcation Canal Canal Canal Structure Wetlands acres 239.8 236.2 215.8 218.7 Marsh acres 43.9 40.3 61.7 60.5 Riparian wetland acres 140.5 143.7 101.9 106.0 Wet meadow acres 55.4 52.2 52.2 52.2 Other Waters acres 443.7 437.2 469.9 476.7 Sensitive Vegetation Alliances Alkali heath marsh acres 0.2 0.2 0.7 0.7 Arrow weed thickets acres 0.4 0.4 0.4 0.4 Black willow thickets acres 124.9 124.9 120.0 119.8 Blue elderberry stands acres 75.4 75.4 75.4 75.4 Button willow thickets acres 1.0 1.2 1.6 1.4 Existing Special Status California bulrush marsh acres 16.9 12.8 24.8 23.6 Environmental Vegetation and California rose briar patches acres 11.1 11.3 13.0 12.5 Conditions Waters Creeping rye grass turfs acres 6.2 6.1 6.1 6.1 Fremont cottonwood forest acres 68.3 68.5 45.3 52.5 Oregon ash groves acres 6.9 7.0 7.0 6.9 Pale spike rush marshes acres 1.6 ------Red willow thickets acres 0.6 0.6 0.6 0.6 Salt grass flats acres 1.4 1.4 1.7 1.7 Silver bush lupine scrub acres 2.0 4.1 4.1 2.0 Spinescale scrub acres 0.1 0.1 0.7 0.7 Tar plant fields acres 33.5 34.9 35.4 33.9 Valley oak woodland acres -- -- 0.2 0.2 Yerba mansa meadows acres 0.8 0.8 0.8 0.8
Mendota Pool Bypass and Reach 2B Improvements Project 3-100 – October 2012 Project Description Technical Memorandum 3.0 Description of Alternatives
Table 3-17 Conditions and Features within the Project Boundaries Compact Fresno Fresno Compact Bypass with Slough Dam Slough Dam Bypass with Wide with Narrow with Wide Units of Narrow Categories Factors Criteria Floodplain Floodplain Floodplain Measure Floodplain and and Short and North and South Bifurcation Canal Canal Canal Structure Special status wildlife habitats Blunt-nosed leopard lizard acres 17.4 15.4 15.4 15.2 Fresno kangaroo rat acres 108.8 111.2 111.2 106.5 Giant garter snake acres 364.9 348.3 436.0 438.9 Greater sandhill crane acres 669.8 635.3 539.9 740.4 Special Status San Joaquin kit fox acres 201.6 197.8 185.6 179.4 Wildlife Swainson's hawk acres 441.4 443.9 366.3 393.5 Existing Valley elderberry longhorn acres 75.4 75.4 75.4 75.4 Environmental beetle Conditions number of Valley elderberry longhorn elderberry 112 113 113 112 beetle shrubs number of Historic Properties listed 3 3 4 4 Cultural and properties1 Historical ranking: 1 (very Maximum Buried Deposits Resources low)-5 (very 4 4 4 4 Sensitivity high)
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 3-101 – October 2012 San Joaquin River Restoration Program
Table 3-17 Conditions and Features within the Project Boundaries Compact Fresno Fresno Compact Bypass with Slough Dam Slough Dam Bypass with Wide with Narrow with Wide Units of Narrow Categories Factors Criteria Floodplain Floodplain Floodplain Measure Floodplain and and Short and North and South Bifurcation Canal Canal Canal Structure Total Farmland in Production acres 1066.9 1302.1 795.7 1620.0 Alfalfa acres 46.5 55.2 21.5 48.3 Existing Almond acres 341.6 512.0 339.7 557.7 Socioeconomics Cotton acres 7.0 7.0 13.4 13.4 Crop Acreage and Economics Grapes acres 242.4 175.6 92.8 271.3 Conditions Other Row Crop acres 166.1 102.5 65.0 200.9 Palm acres 9.7 9.7 9.7 9.7 Pistachio acres 253.7 440.1 253.6 518.6 Primary production (<1.0 feet acres 477 636 528 741 Floodplain inundation at 2,500 cfs) Characteristics Rearing habitat (>1.0 feet acres 385 527 235 319 inundation at 2,500 cfs) Passage Artificial structures across number of Project Fish 20 21 13 13 Conditions for migratory path structures Habitat & Adult Chinook Maximum number of steps at number of Passage 43 67 59 36 Salmon structures jumps Conditions New fish screens along number of Passage 3 4 3 3 migratory path screens Conditions for Juvenile Chinook number of Potential predation sites artificial 21 22 14 14 Salmon structures 1 The number of listed properties is based on records from NRHP National Register of Historic Places, California Register of Historical Resources, Office for Historic Preservation Historic Property Directory, California State Historical Landmarks listing, California Inventory of Historic Resources, California Points of Historical Interest listing, the Caltrans State and Local Bridge Survey, and historical maps, including GLO Plat Maps. No previously recorded National Register or California Register eligible resources were identified in the records search.
Mendota Pool Bypass and Reach 2B Improvements Project 3-102 – October 2012 Project Description Technical Memorandum
4.0 Alternatives Considered and Eliminated from Further Consideration Formulation of a range of Project Alternatives for inclusion in this Project Description TM began with a review of Settlement provisions for achieving the Restoration and Water Management goals and the Settlement provisions for the Reach 2B and Mendota Pool Bypass components. This was followed by preparing the purpose, need, and objectives; developing criteria for including actions in the Project Alternatives; defining planning and implementation constraints; and identifying related projects and opportunities associated with achieving the purpose and need. These steps were applied to actions identified in Settlement provisions and to comments received during the public scoping process to identify a range of alternatives to be addressed. As a result of this process, several potential actions were eliminated from consideration and the reasonable range of Initial Alternatives was identified. This process and the alternatives eliminated from consideration are described in the Alternatives Evaluation TM (Attachment A).
4.1 Pre-Initial Options Analysis
Pre-initial options analysis included concepts suggested during the Project scoping meetings and other concepts suggested within the Project team.
Some actions suggested during the scoping process and considered by the Project Team were retained for inclusion in the Project initial options, while others were not retained for inclusion because they would not meet the Project purposes, needs, goals, and objectives. The suggested actions, and associated screening information, are summarized below.
• Mitigation for flood impacts: No alterations to flood management operations or to the service level of existing flood control facilities (such as design capacity and levee stability) are included in the Project. Mitigation of flood risks not generated by the Project is unwarranted. Local flooding conditions would be improved through increased capacity within the channel and floodplain and improved levees. Alterations to existing flood control facilities (such as the Chowchilla Bifurcation Structure) would provide at least the same level of service as the existing features and would require no changes to operations. • Evaluation and redesign of the Columbia-Mowry Distribution System including facility access, O&M, pumps, pipelines, and power: Modifications to existing canals, pumps, pipelines, access, and power are limited to those relocations necessary to construct the Project. The Project will not include evaluation or redesign of system components outside of those potentially impacted by the Project.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 4-1 – October 2012 San Joaquin River Restoration Program
• No interruption of water deliveries: The Project goals and objectives include diverting water deliveries up to 2,500 cfs within Reach 2B from the San Joaquin River to the Mendota Pool; however, the availability of the contracted water amounts from any particular source is outside the Project purpose. • Acquire land to support recreation, tourism, flora, fauna, and groundwater recharge: The purpose of the Project does not include independently supporting recreation, tourism, flora (other than riparian habitat), fauna (other than salmon and other native fishes), or groundwater recharge, so land would not be acquired solely for these purposes. However, opportunities may exist to support these functions in conjunction with or incidental to implementation of the Project, and land acquired to meet the Project purposes, needs, goals, and objectives may also benefit recreation, tourism, flora, fauna, and groundwater recharge. • Shortening channel distance to reduce levee length and reduce maintenance costs: Shortening of the river channel or the bypass alignments is currently not considered due to the considerable negative effects to habitat, geomorphology, and sediment continuity in the reach that would result from shortening, or straightening, the channel. • Installing a cutoff channel before the river bends just downstream of the Chowchilla Bifurcation Structure to reduce flooding toward Hwy 180: No alterations to flood management operations are included in the Project, and mitigation for flood risks not generated by the Project are unwarranted. Local flooding conditions could be improved through increased capacity within the channel and floodplain and improved levees. • Installing a wall across the river in Reach 3 just below Mendota Dam and diverting water to Mendota Pool: This action would not meet the purpose and need of the Settlement as it would not provide a bypass around the Pool. • Allow salmon in the Pool and Chowchilla Bypass: The extent to which fish would be screened out of the Chowchilla Bypass was not considered as part of this action. Fish screening upstream of Reach 2B diversions to Mendota Pool was included because of high predation risks for juvenile salmon in the Pool due to populations of non-native predators. • Include provisions to allow for Mendota Dam maintenance: Maintenance of Mendota Dam as it relates to operating the Project is included (e.g., removing sediment to operate the Short Canal); however, general maintenance of the structure and it’s equipment are beyond the purpose, need, and scope of the Project. • Avoid bifurcation of future flows: The Settlement requires Restoration Flows in Reach 2B and in downstream reaches, but it does not require flood conveyance in Reach 2B, and diversion of flood flows into the Chowchilla Bypass is required to meet existing flood operation guidelines. The flexibility to divert flows away from the Bypass and to the Pool is also required to meet potential Exchange Contract water deliveries; however, Restoration Flows are required in the Mendota Pool Bypass and downstream reaches.
Mendota Pool Bypass and Reach 2B Improvements Project 4-2 – October 2012 Project Description Technical Memorandum 4.0 Alternatives Considered and Eliminated from Further Consideration
• Fish screens in the Pool: This action would not meet the purpose and need of the Settlement as it would not provide a bypass around the Pool. In addition, the maintenance, cost and reliability of fish screens for all Pool connections would be prohibitively expensive and would not perform as well as other alternatives. • Evaluate all alternatives that avoid impacts to wetlands: The extent of impact to existing wetlands was considered in the alternatives evaluation process. • Avoid dredging or filling in waters of the United States: Filling in waters of the United States would be minimized to the extent possible and was considered in the alternatives evaluation process. • Address effects of the Project on Milburn Pond: The Project does not affect Milburn Pond. • Do not reintroduce salmon in order to protect existing riparian habitat: Existing riparian habitat was considered in the alternatives evaluation process. Not reintroducing salmon would be contrary to the Settlement. Some additional options exist that were not part of the scoping process, but were also considered by the Project Team and not retained for inclusion in the Project initial options because they would not meet the Project purposes, needs, goals, and objectives. These include the following:
• Construction of levees to withstand a 200-year flood: Eliminated because existing levees in the Project area are not part of the Lower San Joaquin River Flood Control Project.
4.2 Pre-Evaluation Screening
During the concept refinement phase of the Project, some of the initial options were revised, refined, or eliminated from further consideration. The concepts considered and eliminated from further consideration prior to the alternatives evaluation are described below. Many concepts were refined or revised during appraisal-level design before moving into the alternatives evaluation; those refinements are described in Attachment A, Section 5.2.
4.2.1 Bottomless Arch Culverts Bottomless arch culverts were considered in the Initial Options TM as a potential method of improving the crossing at San Mateo Avenue. However, based upon further consideration it was decided that bottomless arch culverts would be too difficult to implement in the sand bed channel of Reach 2B because the culverts would require substantial undercut for foundation work, the culverts would potentially require a concrete floor to stabilize the structures during high flows, and could have an unacceptable failure rate. In addition, less expensive and equally beneficial options are available (i.e., concrete box culverts).
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 4-3 – October 2012 San Joaquin River Restoration Program
4.2.2 Corrugated Metal Pipe Culverts Corrugated metal pipe culverts were considered in the Initial Options TM as a potential method of improving the crossing at San Mateo Avenue. However, based upon further consideration it was decided that corrugated metal pipe culverts would be difficult to design for the fish passage requirements and they may have a shortened lifespan due to the corrosive nature of the soils in the Project area.
4.2.3 Bridge A bridge was considered in the Initial Options TM as a potential type of crossing for the San Mateo Avenue crossing. However, based upon further consideration it was found that both a box culvert crossing and a bridge crossing are capable of meeting the fish passage requirements, but the bridge is significantly more expensive. Therefore, the bridge crossing was eliminated from further consideration.
4.2.4 Floodplain Vegetation Types In the Initial Options TM, several floodplain vegetation types were considered: fully grassed floodplain, forested riparian fringe along the river with a grassed floodplain, and fully forested floodplain. Based upon further review during concept refinement, the floodplain vegetation concept used in the hydraulics modeling was revised to a mosaic type floodplain habitat including a forested riparian fringe along the river and a mixture of grasslands, scrub, and trees on the floodplain. The mosaic floodplain habitat was more typically found along the river historically and can be found in other parts of the San Joaquin Valley today.
4.2.5 Floodplain Recontouring As part of the Initial Options development, recontouring of the entire floodplain to allow inundation of large areas at lower flows was considered. Based upon further review during concept refinement, this concept provided less or similar benefit as the select floodplain grading included in the Project Alternatives. Wholesale recontouring would not increase the habitat diversity on the floodplain and thus would not provide increased benefits to fish. However, it would require excavation of much larger quantities of material and thus would increase costs. Wholesale recontouring also has the potential to decrease the area of inundation and cause erosion along the channel. Wholesale floodplain recontouring was therefore eliminated from further consideration.
4.2.6 Older Levee Setbacks During concept refinement, the levee alignments presented in the Initial Options TM were refined and revised and one alignment was eliminated: Initial Option FP-1. Initial Option FP-1 was found to not sufficiently meet the Settlement requirements to provide floodplain and riparian habitat in Reach 2B. The other levee alignments were modified to account for property lines, field lines, infrastructure, flow and sediment continuity purposes, and to add a minimum 300-foot buffer, where appropriate, between the channel and levee to protect the levee from lateral channel migration and erosion.
4.2.7 Mendota Dam Removal The Fisheries Management Workgroup asked the Project to consider removing Mendota Dam as part of the Fresno Slough Dam Initial Alternative. Based upon further
Mendota Pool Bypass and Reach 2B Improvements Project 4-4 – October 2012 Project Description Technical Memorandum 4.0 Alternatives Considered and Eliminated from Further Consideration
consideration and analysis, it was decided that the Project would not remove the dam because it provides a grade control point between Reach 3 and Reach 2B. Without the dam, the channel base level would be lowered and incision could migrate upstream through Reach 2B (Tetra Tech 2011a). This could jeopardize passage conditions at the structures in the Project area such as at San Mateo Avenue and Chowchilla Bifurcation Structure where channel grades would potentially be lowered by up to approximately 4.7 feet and 1.9 feet, respectively, effectively relocating the grade-control point. Lowering the base-level would also eliminate overbank flow during all but the highest flows (Tetra Tech 2011a). Furthermore, structural stability of existing and proposed structures could be compromised by the decreased bed elevations and resulting scour.
4.2.8 Channel Grading from Reach 3 to Chowchilla Bifurcation Structure The Technical Advisory Committee requested that the Project consider not constructing grade control structures in the Mendota Pool Bypass channel and that the channel be graded from the confluence with Reach 3 at an appropriate slope. Based upon further analysis, it was found that grading the channel at the equilibrium slope starting at the confluence with Reach 3 would lower the entire Mendota Pool Bypass Channel and Reach 2B channel up to approximately 14.3 feet and 11.7 feet, respectively, and that the new base elevation would require excavation (or result in erosion) all the way up to the Chowchilla Bifurcation Structure, which would serve as a grade control point. Furthermore, it was found that this would leave the Reach 2B channel elevation approximately up to 5.3 feet below the floor elevation of the Chowchilla Bifurcation Structure potentially undermining the structure and presenting a fish passage barrier as well as disconnecting the channel from its floodplain throughout Reach 2B (Tetra Tech 2011b). Based upon the necessary structural improvements at the Chowchilla Bifurcation Structure to prevent failure, the fish passage impacts, the significant decrease in floodplain inundation area and frequency, the surplus of cut material for the bypass channel, and water quality/stability concerns from eroding channel bed and banks, this concept was eliminated from further consideration.
4.2.9 Floating Picket Weir A floating picket weir was considered in the Initial Options TM as a potential method of providing a fish exclusion barrier at the downstream end of the Mendota Pool Bypass Channel to direct fish into the Bypass. Based upon further consideration, this option was eliminated due to the magnitude of flows expected to be seen at the barrier location and this type of weir not being appropriate for such high flows.
4.2.10 Behavioral Barrier Behavioral fish barriers were investigated during the appraisal-level design as a means of providing an exclusion/directional barrier at the downstream end of the Mendota Pool Bypass Channel to direct upmigrating adult salmon into the bypass channel and away from the base of Mendota Dam. A system to reroute irrigation flows from Mendota Dam to downstream of the barrier would be included with this concept, leaving slack water between the end of the bypass channel and the Dam. Behavioral barrier systems are a developing technology, but two main types of barriers have been implemented on other rivers: electric barriers and acoustic barriers. Both types of barriers have significant draw-backs for implementation in the Project.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 4-5 – October 2012 San Joaquin River Restoration Program
Electric barriers generate an electric current through the water across a channel in order to deter fish. Based on existing and previous installations, electric barriers were found to present potential unavoidable electric shock hazards for fish (target and non-target species), other animals, people, and watercraft. Often target fish species either made it past the barrier or were killed. Velocities and depths need to be consistent for the barrier to be effective; something that has proven difficult on reaches with moveable beds and those with variable flows. Velocities also need to be sufficient to sweep stunned fish out of the barrier, which may be difficult in the low slope, low velocity Reach 3. Some programs are considering replacing their electric barriers with different technologies. For all these reasons, the electric barrier is not recommended.
Acoustic barriers use a sound signal contained in a bubble curtain of air to deter fish; acoustic barriers may also incorporate the use of strobes and lights to deter fish. There are few existing installations of acoustic barriers, but they have been found to be most effective on juvenile fish with minimal effectiveness on adult fish. Effectiveness has also been found to decrease with increasing flows. Acoustic barrier technology is not capable of functioning during high flows such as flood releases from Pine Flat routed down Fresno Slough into Reach 3 (typically at 4,500 cfs or reach capacity). These high flows occur on an average annual frequency of 1 in 5 years, typically in wet years. Since the purpose of the Mendota Pool Bypass Barrier is to direct adult migrating salmon into the bypass at all flows, including flood flows, the acoustic barrier is not recommended.
4.2.11 Velocity Barrier Based on design and hydraulic analyses, a velocity barrier at the downstream end of the Mendota Pool Bypass Channel was eliminated from further consideration because the resulting barrier would be higher than Mendota Dam, would increase the elevation in Mendota Pool between 4 and 5 feet, and would necessitate improvements to all levees on Mendota Pool and Fresno Slough.
4.2.12 Other Types of Fish Screens During the appraisal-level design several types of fish screens were reviewed for their applicability to the Project for screening fish from the 2,500 cfs diversion to Mendota Pool. The following screen design types were eliminated from further consideration due to design constraints. Horizontal flat plate screens (patented by Farmers Irrigation District, OR) were eliminated because they are intended for use with smaller diversions (less than 100 cfs); there are no physical model studies or field applications demonstrating that this design is capable of handling larger diversions. Travelling screens were eliminated because maintenance is a significant problem, and there are no known field applications for diversions of the Project’s size. Box screens were eliminated because, while they can be sized for larger applications, they function very similarly to cylindrical screens which were considered further. Pump screens were eliminated because they are only applicable to very small diversions (less than 10 cfs).
4.2.13 Pump Diversion to Mendota Pool All the proposed Alternatives divert water to Mendota Pool via gravity. During the appraisal-level design, a pump diversion was also considered and preliminary costs were developed. The pump diversion was eliminated from further consideration because the
Mendota Pool Bypass and Reach 2B Improvements Project 4-6 – October 2012 Project Description Technical Memorandum 4.0 Alternatives Considered and Eliminated from Further Consideration
capital improvement costs are nearly four times the cost of the gravity diversions. In addition, the pump diversion would rely on Mendota Dam or another barrier to form a backwatered pool, so the pump diversion would not be able to eliminate the need for a fish passage structure.
4.3 Initial Alternatives Screening
Two Floodplain Initial Alternatives and two Bypass Initial Alternatives were included in the Project Description based on their comparatively better performance in the alternatives evaluation. The included alternatives were FP-2 (now called the Narrow Floodplain), FP-4 (now called the Wide Floodplain), Compact Bypass, and Fresno Slough Dam. The results of the alternatives evaluation and the Initial Alternatives recommended for elimination are described in Section 8.0 of Attachment A.
Three Initial Alternatives were eliminated from consideration based on the evaluation results: FP-1, FP-5, and the Settlement Alignment. These Initial Alternatives were eliminated because they perform relatively poorly when compared to the other Initial Alternatives. The remaining Initial Alternatives (FP-2, FP-3, FP-4, Compact Alignment, and Fresno Slough Dam) provide a better balance between benefits and impacts.
FP-1 would result in a confined channel system with high velocities and scour along the corridor requiring expensive bank revetment. Vegetation could be difficult to establish, and water depths would often be too deep to provide effective floodplain rearing and primary production benefits. Based on the results of the evaluation, FP-1 performs poorly for several reasons:
• Relatively low amounts of rearing habitat • Poor quality shallow water habitat • Relatively high capital improvement costs • Relatively low amounts of restoration area • Relatively greater risk of channel instability • Relatively larger nuisance seepage impacts
FP-5 would result in large areas too shallow and dry to provide effective floodplain rearing and primary production benefits. Based on the results of the evaluation, FP-5 performs poorly for several reasons:
• Poor quality shallow water habitat • Relatively high restoration and land costs • Relatively greater land removed from production • Limited additional fish habitat and passage benefits for the added costs • Potential for fish strandings
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 4-7 – October 2012 San Joaquin River Restoration Program
The Settlement Alignment provides less habitat than the Compact Alignment but with higher costs and larger land requirements. Based on the results of the evaluation, the Settlement Alignment performs poorly for several reasons:
• No additional shallow water or rearing habitat • Relatively high capital improvement costs • Relatively less restoration area • Relatively greater risk of channel instability • Relatively greater land removed from production
One option was recommended for elimination from consideration based on the evaluation results: Bend 10 Columbia Canal Relocation. This option was recommended for elimination because it performs relatively poorly when compared to the Bend 10 levee revetment, which provides a better balance between benefits and impacts.
Based on the results of the evaluation, the Bend 10 Columbia Canal Relocation option performs poorly for several reasons:
• Additional land acquisition is required • More land removed from production • Relatively greater environmental impacts
Mendota Pool Bypass and Reach 2B Improvements Project 4-8 – October 2012 Project Description Technical Memorandum
5.0 Project Implementation The purpose of this section is to identify permits and approvals required for implementation of the Project. Table 5-1 provides planning information for the permitting process, including the recommended prerequisites for application, the estimated time for processing, and the estimated fee. Federal, State, and local actions are described in the sections below in reference to their application to the Project and the permit purpose and requirements. In general, all Federal and State actions (permit issuance) will require a signed Record of Decision/Notice of Determination. Additional information on permit acquisition procedures, submittal package requirements, critical issues, timing, and permit fees is discussed in detail in the Regulatory Compliance TM (SJRRP 2010b).
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 5-1 – October 2012 San Joaquin River Restoration Program
Table 5-1 Summary of Permits and Approvals Required for the Project Agency and Associated Recommended Estimated Lead Permit or Prerequisites for Processing Anticipated Agency for Approval Submittal1 Time2 Fees Submittal Federal USACE Section 404 and Section 10 8 months $100 for Reclamation Clean Water Act Individual permit Section 404 • Application is waived for Individual Permit • Biological Assessment for governmental Rivers and submittal to USFWS/NMFS agencies (none) Harbors Act • Section 401 Water Quality Section 10 Permit Certification permit or Rivers and application Harbors Act • Draft NEPA document Section 14 Permit • Section 106 compliance (Section 408) documentation • Wetland delineation • Alternatives analysis • Mitigation and Monitoring Plan Section 408 • Written request for approval of the Federal flood control project modification • Technical analyses and demonstration of adequate design • Description and maps of lands, easements, and right- of-way owned by the Federal project and required for the modification • Discussion of residual risk • Administrative record of decisions related to the Project proposal • Justification to construct in the floodplain • Demonstration of environmental protection compliance USFWS/NMFS • Ongoing technical assistance 135 days None Reclamation Endangered (pre-consultation) Species Act • Biological Assessment Section 7 • EFH Assessment Consultation Magnuson- Stevens Fisheries Conservation and Management Act
Mendota Pool Bypass and Reach 2B Improvements Project 5-2 – October 2012 Project Description Technical Memorandum 5.0 Project Implementation
Table 5-1 Summary of Permits and Approvals Required for the Project Agency and Associated Recommended Estimated Lead Permit or Prerequisites for Processing Anticipated Agency for Approval Submittal1 Time2 Fees Submittal USFWS/NMFS • Ongoing informal technical N/A None USFWS/NMFS Fish and Wildlife consultation Coordination Act • Biological impact Report assessments (as addressed in TM 2.3 Environmental Field Survey Report) SHPO/ACHP • Cultural Resources Survey 18 months None Reclamation National Historic and Evaluation Report (if Preservation Act, mitigation is necessary to Section 106 resolve adverse effects to historic properties, then additional reports would be required for SHPO consultation that detail the results of these efforts) U.S. Coast Guard • Bridge design 3 months None Reclamation General Bridge Act • Fish and Game Code and Rivers and Section 1602 Notification or Harbors Act Alteration Agreement Section 9 • CWA Section 404 permit or application • Draft NEPA Document • Section 401 Water Quality Certification application • Biological Assessment for submittal to USFWS/NMFS or Biological Opinion State CVRWQCB • Application 2 months $500 or more Reclamation/ Clean Water Act • Fish and Game Code DWR Section 401 Water Section 1602 Notification or Quality Alteration Agreement Certification • CWA Section 404 permit or application • Draft CEQA Document • Mitigation and Monitoring Plan SWRCB/ • Permit Registration 1 to 2 weeks Up to $3,192 Reclamation/ CVRWQCB Documents DWR Clean Water Act • Design drawings (for Section 402 SWPPP) Construction General Permit
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 5-3 – October 2012 San Joaquin River Restoration Program
Table 5-1 Summary of Permits and Approvals Required for the Project Agency and Associated Recommended Estimated Lead Permit or Prerequisites for Processing Anticipated Agency for Approval Submittal1 Time2 Fees Submittal DFG • Informal technical 30 days for None DWR California consultation consistency Endangered • Biological Opinion, if determination, if Species Act requesting a consistency appropriate Section determination 6 months for 2080.1 • Biological document for 2081 incidental take Consistency Permit, if requesting statement Determination incidental take statement 2081 Incidental Take Statement DFG • Application 3 months Up to $4,482.75 DWR Fish and Game • Section 401 Water Quality Code Section 1602 Certification permit or Streambed application Alteration • CWA Section 404 permit or Agreement application • Final CEQA Document and Mitigation Plan CVFPB • Application 2 months None DWR California Code of • Section 401 Water Quality Regulations, Certification permit or Title 23: application Encroachment • CWA Section 404 permit or Permit application • Draft CEQA Document and Mitigation Plan • Fish and Game Code Section 1602 Notification or Alteration Agreement • Biological Assessment for submittal to USFWS/NMFS or Biological Opinion SWRCB • Application 3 months $200 or more Reclamation/ Amended water • Draft (possibly Final) CEQA DWR right Document State Lands • Application 4 to 5 months $25 application Reclamation/ Commission • Draft CEQA Document fee and possible DWR Land Use Lease • Property ownership leasing fees determination
Mendota Pool Bypass and Reach 2B Improvements Project 5-4 – October 2012 Project Description Technical Memorandum 5.0 Project Implementation
Table 5-1 Summary of Permits and Approvals Required for the Project Agency and Associated Recommended Estimated Lead Permit or Prerequisites for Processing Anticipated Agency for Approval Submittal1 Time2 Fees Submittal Local SJVAPCD • AIA Application 1.5 months for $700 for Air Reclamation/ Air Impact Analysis • Dust Control Impact Analysis DWR AIA Monitoring and Reporting 3 Regulation VIII Schedule Plan and Air application Dust Control Plan • AIA Fee Deferral Schedule Impact Analysis $350 to process Federal Clean Air • Dust Control Plan Dust Control Plan Act • Dust Control Training Course $177 for • Pre-application meeting Portable (encouraged) Equipment • List of construction Registration equipment that may require Portable Equipment Registration Fresno/Madera • Permit application 3 months Varies DWR Counties • Reclamation plan SMARA Fresno/Madera • Copy of applicable contracts 2 months None DWR Counties Williamson Act Contracts 1 Items listed are the items recommended for submittal of the specified application, not for approval. Several permits require additional items for permit approval (e.g., signed Record of Decision/Notice of Determination). Requirements for approval are discussed within the corresponding section of the document. 2 Anticipated processing time is estimated based on the period from verified submission of completed application documents to permit issuance. 3 The $700 filing fee has been paid as part of the AIA submittal for the SJRRP. ACHP = Advisory Council on Historic Preservation AIA = Air Impact Assessment DFG = California Department of Fish and Game CEQA = California Environmental Quality Act of 1970 CVFPB = Central Valley Flood Protection Board CVRWQCB = Central Valley Regional Water Quality Control Board CWA = Clean Water Act DWR = California Department of Water Resources EFH = essential fish habitat NEPA = National Environmental Policy Act of 1969 NMFS = National Marine Fisheries Service SHPO = State Historic Preservation Officer SJVAPCD = San Joaquin Valley Air Pollution Control District SJRRP = San Joaquin River Restoration Program SMARA = Surface Mining and Reclamation Act of 1975 SWPPP – storm water pollution prevention plan SWRCB = State Water Resources Control Board USACE = U.S. Army Corps of Engineers USFWS = U.S. Fish and Wildlife Service
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 5-5 – October 2012 San Joaquin River Restoration Program
5.1 Federal Actions
5.1.1 U.S. Army Corps of Engineers Regulations
Application to Proposed Action The proposed action would result in fill and/or dredge of jurisdictional waters of the United States, including wetlands, especially within the San Joaquin River during any in- river construction activities (e.g., levee removal and construction of the San Mateo Avenue crossing) and at other locations, including Fresno Slough and Little San Joaquin Slough. As a result, this Project will require authorization from USACE pursuant to Section 404 of the Clean Water Act (CWA).
In addition to affecting waters of the United States, the proposed action would also result in construction in, over, or under; excavation of material from; or deposition of material into “navigable waters,” such as the San Joaquin River. As a result, the Project will require authorization from USACE pursuant to Section 10 of the Rivers and Harbors Act (RHA) (33 USC 403) for the construction of certain elements of the Project.
Additionally, since the Project would alter a Federal flood control project by potentially relocating or modifying an existing Federal project levee, USACE approval under Section 14 of the RHA (33 USC 408, referred to as Section 408) or under Section 208.10 (33 CFR 208.10) is required prior to proceeding with the Project.
Permit Purpose and Requirements CWA Section 404 establishes a program to regulate the discharge of dredged material or placement of fill material into waters of the United States, including wetlands. Waters of the United States include surface waters such as navigable waters and their tributaries, all interstate waters and their tributaries, natural lakes, all wetlands adjacent to other waters, and all impoundments of these waters. Activities that require a permit under Section 404 include, but are not limited to, placing fill or riprap, grading, mechanized land clearing, and dredging in waters of the United States. Any activity that results in the deposit of dredged or fill material within the ordinary high-water mark of waters of the United States usually requires a permit, even if the area is dry when the activity takes place.
The USACE Regulatory Branch issues several types of Section 404 permits. Those most applicable to the proposed action are Nationwide Permits (NWPs) and Individual Permits. Projects with only minimal adverse effects (i.e., fills of less than 0.5 acre of nontidal waters of the United States) can typically be authorized under USACE’s NWP program to expedite the environmental compliance process, provided the Project satisfies the terms and conditions of the particular NWP. Since the proposed Project would have more than minimal impacts, it would require an Individual Permit.
The CWA and guidelines outlined in a Memorandum of Agreement (MOA) between the U.S. EPA and USACE dated November 15, 1989, set forth a goal of restoring and maintaining existing aquatic resources. This MOA directs USACE to strive to avoid adverse impacts and offset unavoidable adverse impacts to existing aquatic resources, and for wetlands, to strive to achieve a goal of no overall net loss of values and functions. The
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MOA also noted the value of other waters of the United States, including streams, rivers, and lakes. Under the guidelines, all jurisdictional waters of the United States are afforded protection and requirements are outlined for practicable mitigation based on values and functions of the aquatic resources that will be affected.
U.S. EPA develops regulations with which USACE must comply and reviews the permits issued by USACE. Section 404(c) of the CWA authorizes U.S. EPA to veto a USACE decision to issue a permit if a proposed action “will have an unacceptable effect on municipal water supplies, shellfish beds and fishery areas, wildlife, or recreational areas.”
Section 10 of the RHA (33 USC 403) requires authorization from USACE for any work in navigable waters including the construction of any structure over, in, and under navigable waters of the United States. In addition, authorization is required for excavation/dredging or deposition of material or any obstruction or alteration in a navigable water. Navigable waters are those subject to the ebb and flow of the tide and those that are currently used, have been used in the past, or may be susceptible to use to transport interstate or foreign commerce (55 CFR 329.4). They include coastal and inland waters, lakes, rivers, and streams that are navigable, and the territorial seas. Structures or work outside the limits defined for navigable waters would require a Section 10 permit if the structure or work affects the course, location, condition, or capacity of the water body.
Section 208.10 (33 CFR 208.10) provides regulations regarding encroachments on Federal flood control structures and facilities that are constructed for local flood protection. Minor, low impact modifications of Federal flood control projects which do not adversely affect the function of the protective system can be approved by the USACE under Section 208.10. These modifications cannot change the authorized geometry or the hydraulic capacity of the Federal project. Small alterations are typically approved under a Central Valley Flood Protection Board (CVFPB) Encroachment Permit (see Section 4.5) and are reviewed and approved by the USACE in accordance with Section 208.10.
Major alterations to a Federal flood control project, including alterations to channels and levees that change the Federal project’s authorized geometry or the hydraulic capacity, would require a Section 408 permit. Section 408 requires authorization from USACE for the alteration of any sea wall, bulkhead, jetty, dike, levee, wharf, pier, or other work built by a Federal agency for the preservation and improvement of any of its navigable waters or to prevent floods. The types of alterations or modifications that require Section 408 approval include degradations, raisings, and realignments to the flood protection system or any modification where engineering analysis indicates that the system performance is adversely impacted. To receive authorization, the applicant must establish that the proposed alteration will not be injurious to the public interest and will not impair the usefulness of such work.
The USACE would initiate formal actions under Section 408 and Section 208.10 at the request of the CVFPB. The USACE is also consulted prior to initiating formal actions.
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5.1.2 Federal Endangered Species Act
Application to Proposed Action Several species that are Federally listed as threatened or endangered potentially occur in the Project area. As described in the TM on Existing Environmental Conditions for the Project, implementation of the proposed action may result in adverse effects to these species or their habitat. Because the action is proposed by a Federal agency and requires Federal permits and approvals, and because Project implementation could adversely affect Federally listed species, Section 7 consultation with USFWS and NMFS is required. The lead agency will prepare a Biological Assessment to obtain concurrence or a Biological Opinion (with incidental take statements, as necessary) from USFWS and NMFS for the proposed action.
Under the Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA), NMFS regulates essential fish habitat (EFH). Since the proposed action may have adverse effects to EFH, the lead agency will need to consult with NMFS under the MSFCMA along with the Section 7 consultation.
Permit Purpose and Requirements The ESA of 1973, as amended (16 USC 1531 et seq.), is a mechanism for the protection and recovery of species threatened with extinction and includes, but is not limited to, the following:
• a process to list species in danger of becoming extinct (Section 4) • a prohibition on “take” of threatened and endangered species (Section 9) • processes for exemption from Section 9 take prohibitions when take is incidental to, and not the purpose of, otherwise lawful activities (Section 7 and Section 10) The ESA is administered by USFWS and NMFS. USFWS is responsible for protection of birds, terrestrial, and resident (nonanadromous) freshwater species. NMFS is responsible for protection of marine species and anadromous fish.
Section 9 of the ESA prohibits “take” (i.e., harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or attempt to engage in any such conduct) of any threatened or endangered species. Harm is further defined to include significant habitat modification or degradation that results in death or injury to listed species by significantly impairing behavioral patterns such as breeding, feeding, or sheltering.
Section 7 of the ESA outlines procedures for Federal interagency cooperation to conserve Federally listed species and designated critical habitat. ESA mandates that all Federal agencies participate in the conservation and recovery of listed threatened and endangered species and that each agency ensure that any action it authorizes, funds, or carries out does not jeopardize the continued existence of a listed species or its critical habitat. Critical habitat is identified as specific areas that have the physical and biological features that are essential to the conservation of a listed species, and that may require special management considerations for protection. Section 7 outlines the required consultation procedures that provide Federal agencies with a mechanism for “incidental
Mendota Pool Bypass and Reach 2B Improvements Project 5-8 – October 2012 Project Description Technical Memorandum 5.0 Project Implementation take,” provided the “taking” will not jeopardize the continued existence of any listed species, or destroy or adversely modify critical habitat. Depending upon the anticipated level of impact to Federally listed species, the Federal lead agency and the USFWS and/or NMFS will engage in different levels of consultation:
• If the Federal lead agency finds that the Project would have “no effect” on listed species, no formal consultation is initiated with USFWS or NMFS • If the Federal lead agency finds that the Project is “not likely to adversely affect” listed species, informal consultation with USFWS and/or NMFS would be initiated by the Federal lead agency to determine appropriate avoidance and minimization measures (e.g., best management practices [BMPs]) for the Project. The desired outcome of informal consultation is a letter of concurrence from USFWS and/or NMFS with the findings presented by the Federal lead agency • If the Federal lead agency finds that the Project is “likely to adversely affect” a listed species, formal consultation is initiated with USFWS and/or NMFS. After determining whether the Project would jeopardize the continued existence of a listed species, the USFWS and/or NMFS would render either a jeopardy or nonjeopardy determination. The desired outcome of formal consultation is a signed nonjeopardy Biological Opinion, issued by USFWS and/or NMFS, stating the acceptable level of impact to listed species, the conservation measures for the species, and the agreed upon mitigation ratios for anticipated impacts. A signed Biological Opinion would include a statement authorizing take of species that may occur as incidental to an otherwise legal activity (i.e., incidental take statement) and is issued on the basis of information provided to USFWS or NMFS by a lead agency, often in the form of a Biological Assessment, prepared by either the Federal lead agency or the applicant The MSFCMA, also known as the Sustainable Fisheries Act (16 USC Section 1801 et seq.), requires NMFS and the eight regional Fishery Management Councils to minimize, to the extent practicable, adverse effects to EFH. EFH is defined as the waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity (50 CFR 600 et seq.). The EFH provisions of the MSFCMA are designed to protect fisheries habitat from being lost due to disturbance and degradation. NMFS and the regional Fishery Management Councils identify and describe EFH for each of the commercially managed marine and anadromous fish species in published fishery management plans.
The MSFCMA requires all Federal agencies to consult with NMFS (under the stewardship of the Secretary of Commerce) on activities or proposed activities that are authorized, funded, or undertaken by that agency that may adversely affect EFH. NMFS must then provide conservation recommendations to conserve and reduce impacts to EFH. These recommendations may include measures to avoid, minimize, mitigate, or otherwise offset adverse effects on EFH. Federal agencies are required to respond to EFH Conservation Recommendations.
Guidelines from the MSFCMA direct NMFS to use a coordinated process to evaluate projects that may affect EFH under Section 305(b) of the MSFCMA (16 USC
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Section 1855[b]; 50 CFR 600 et seq.). EFH consultation would be included with the Section 7 consultation (16 USC Section 1536).
5.1.3 Fish and Wildlife Coordination Act
Application to Proposed Action The Fish and Wildlife Coordination Act (FWCA) requires Federal agencies to consult with USFWS, NMFS, and DFG before undertaking or approving water projects that would control or modify surface water. Because the proposed action would affect surface waters, the lead agency must conduct consultation pursuant to the FWCA.
Purpose and Requirements Coordination under FWCA is intended to promote conservation of fish and wildlife habitats by preventing their loss or damage and to provide for development and improvement of fish and wildlife habitats in connection with water projects. Federal agencies undertaking water projects are required to fully consider recommendations made by USFWS, NMFS, and DFG in project reports and include measures in project plans to reduce impacts on fish and wildlife habitat. Documentation of compliance with FWCA is a separate analysis of habitats of concern to USFWS and DFG and does not replace the analysis required by Section 7 of the Federal ESA. The process will, however, help to ensure that impacts to species protected under the Migratory Bird Treaty Act and the Bald Eagle Protection Act (see Section 6.1.1 and 6.1.2) are considered and avoided as required by law.
5.1.4 National Historic Preservation Act, Section 106
Application to Proposed Action The proposed action may affect properties that are listed or eligible for listing on the National Register of Historic Places (NRHP) (16 U.S.C. 470 as amended).
Purpose and Requirements Section 106 of the National Historic Preservation Act (NHPA) and implementing regulations at 36 CFR Part 800 require Federal agencies to take into account the effects of their undertakings on cultural resources (which include archaeological and architectural resources, and traditional cultural properties) that are listed on, are eligible for listing on, or are potentially eligible for listing on the NRHP. During this process, the Federal agency is usually required to consult with the State Historic Preservation Officer (SHPO) and in some instances the Advisory Council on Historic Preservation (ACHP), an independent Federal agency that advises the President and Congress on national historic preservation policy and administers the NHPA’s Section 106 review process. Section 101 of the NHPA establishes the responsibilities of the SHPO, which include consulting with Federal agencies regarding undertakings that may affect historic properties. The NHPA also requires that, in carrying out the requirements of Section 106, each federal agency must consult with any Indian tribe that attaches religious and cultural significance to historic properties that may be affected by the agency’s undertakings.
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5.1.5 Rivers and Harbors Act Section 9 and General Bridge Act of 1946
Application to Proposed Action The General Bridge Act of 1946, as amended, and Section 9 of the RHA, as amended, require that the location and plans of bridges and causeways across the navigable waters of the United States be submitted to and approved by the Secretary of Transportation prior to construction. The proposed Project will likely require the construction of a bridge at the intersection of San Mateo Avenue and the San Joaquin River; therefore, the lead agency will need to apply for a bridge permit.
Permit Purpose and Requirements The purpose of regulating bridge construction under the General Bridge Act and Section 9 of the RHA is to preserve the public right of navigation and to prevent interference with interstate and foreign commerce. The authority to issue bridge permits was delegated by the Secretary of Transportation to the Commandant, U.S. Coast Guard, by Department of Transportation Order 1100.1 dated 31 March 1967 (49 CFR 1.46(c)). Project information and details about the proposed bridge must be submitted to the Commandant for approval prior to the construction of a bridge over navigable waters.
5.2 State Actions
5.2.1 Clean Water Act Section 401
Application to Proposed Action The proposed action will result in fill and/or dredging of jurisdictional waters of the State, including wetlands, particularly in the San Joaquin River and nearby channels such as the Fresno Slough and Little San Joaquin Slough. As a result, a Section 401 Water Quality Certification will be required for these actions.
Permit Purpose and Requirements Under Section 401 of the CWA, an applicant for a Section 404 permit must obtain a certificate from the USEPA or their delegated authority (in California, the SWRCB is delegated by EPA to administer the 401 Program) stating that proposed fill is consistent with the State’s water quality standards and criteria. In California, the authority to grant water quality certification is delegated by the State Water Resources Control Board (SWRCB) to the nine Regional Water Quality Control Boards (RWQCBs). Due to its location, the Project falls under jurisdiction of the Central Valley Regional Water Quality Control Board (CVRWQCB); therefore, the lead agency will consult with the CVRWQCB to obtain a Section 401 Water Quality Certification.
5.2.2 Clean Water Act Section 402
Application to Proposed Action The proposed action would result in discharges of waste into waters of the State, which include “any surface water or ground water, including saline waters, within the
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boundaries of the State.” An NPDES permit will be required for construction-related discharges to surface waters.
Permit Purpose and Requirements Dischargers whose projects disturb 1 or more acres of soil or whose projects disturb less than 1 acre but are part of a larger common plan of development that in total disturbs 1 or more acres, are required to obtain coverage under the General Permit for Stormwater Discharges Associated with Construction and Land Disturbance Activity (Construction General Permit, 2009-0009-DWQ). Construction activity subject to this permit includes clearing, grading, and disturbances to the ground such as stockpiling or excavation, but does not include regular maintenance activities performed to restore the original line, grade, or capacity of the facility. In California, the authority to regulate compliance with CWA Section 402 requirements is shared between the SWRCB and the nine RWQCBs. Most enforcement responsibilities are delegated to the RWQCBs; therefore, the lead agency will coordinate with the CVRWQCB to ensure compliance.
To acquire a Construction General Permit, applicants must submit Permit Registration Documents (PRDs), including an NOI Form to discharge stormwater, a Storm Water Pollution Prevention Plan (SWPPP), and other documents. The SWPPP must be prepared by a Qualified SWPPP Developer and must list BMPs the discharger will use to protect stormwater runoff. Implementation of these BMPs must be overseen by a Qualified SWPPP Practitioner.
Compliance with the General Permit also requires on-site visual monitoring of stormwater and non–stormwater discharges and the submission of annual reports throughout the duration of the Project. Depending on the risk level of the Project, additional effluent monitoring or bioassessment sampling may be required. Once the Project is complete, the applicant must submit a Notice of Termination to be approved by the RWQCB.
5.2.3 California Endangered Species Act
Application to Proposed Action Several State-listed threatened or endangered species potentially occur in the Project area and particularly near the San Joaquin River and in adjacent waterways such as the Fresno Slough, Little San Joaquin Slough, and the Mendota Pool. Implementation of the proposed action may result in adverse effects to these species or their habitat. For species listed as “Fully Protected,” DFG cannot issue take authorization and requires the Project proponent to completely avoid these species.
Permit Purpose and Requirements CESA (Fish and Game Code Section 2050 et seq.) generally parallels the main provisions of the Federal ESA and is administered by DFG. Under CESA, the term “endangered species” is defined as a species of plant, fish, or wildlife that is “in serious danger of becoming extinct throughout all, or a significant portion of, its range” and is limited to species or subspecies native to California.
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CESA establishes a petitioning process for the listing of threatened or endangered species. The California Fish and Game Commission is required to adopt regulations for this process and establish criteria for determining whether a species is endangered or threatened. The California Code of Regulations, Title 14, Section 670.1(a) sets forth the required contents for such a petition. CESA prohibits the “taking” of listed species except as otherwise provided in State law. Unlike its Federal counterpart, CESA applies the take prohibitions to species petitioned for listing (State candidates). Section 86 of the Fish and Game Code defines “take” as to “hunt, pursue, catch, capture, or kill, or attempt to hunt, pursue, catch, capture, or kill.”
Sections 2080 and 2081 of the Fish and Game Code cover the “take” of State threatened and endangered species. One of two CESA-compliance processes is generally followed when take of a State-listed species may occur, the Section 2080.1 consistency determination or Section 2081 incidental take permit processes. If all listed species potentially affected by the proposed action are protected under both the Federal ESA and CESA, the California legislation encourages cooperative and simultaneous consultation between USFWS and DFG to coordinate the Federal ESA Section 7 process (see Section 5.1.2) and the CESA process so that consistent and compatible findings result. In this circumstance, authorization for take under CESA would be provided by a Section 2080.1 consistency determination. Section 2080.1 allows an applicant who has obtained a Federal incidental take statement through Section 7 consultation to request that DFG issue a consistency determination stating that the Federal document is “consistent” with CESA. A Section 2081 incidental take permit is required if agreement cannot be reached about consistency, for example if the Biological Opinion allows for incidental take of a fully protected species or if the project may affect a species that is only listed by the State.
5.2.4 California Fish and Game Code Section 1602
Application to Proposed Action The proposed action will substantially divert or obstruct the natural flow or substantially change the bed, channel, or bank of a river, stream, or lake or use materials from a streambed. As a result, a notification of Streambed Alteration Agreement pursuant to Section 1600 et seq. of the Fish and Game Code must be submitted for this Project.
Permit Purpose and Requirements DFG’s Lake and Streambed Alteration Program (Fish and Game Code Section 1600 et. seq.) requires any person, State or local governmental agency, or any public utility who proposes a project that will substantially divert or obstruct the natural flow or substantially change the bed, channel, or bank of any river, stream, or lake or use materials from a streambed to notify DFG.
Notification is generally required for any project that will take place in or in the vicinity of a river, stream, lake, or their tributaries. This includes rivers or streams that flow at least periodically or permanently through a bed or channel with banks and support fish or other aquatic life, and watercourses having a surface or subsurface flow that supports or has supported riparian vegetation.
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After DFG determines that the Project will need a Lake or Streambed Alteration Agreement, Project activities within jurisdictional waters may not begin until a Lake or Streambed Alteration Agreement is developed and the Project described in that agreement is reviewed under CEQA. By working with DFG to develop a draft Lake or Streambed Alteration Agreement, the Project applicant can modify the Project features to avoid or lessen potential impacts on fish and wildlife resources. This would simplify CEQA review of the Project and expedite the issuance of a final agreement.
5.2.5 California Code of Regulations, Title 23
Application to Proposed Action A permit is required for any project or plan of work that is: (1) within Federal flood control project levees and within a CVFPB easement, (2) or may have an effect on the flood control functions of project levees, (3) or is within a CVFPB designated floodway, (4) or is within regulated Central Valley streams listed in Table 8.1 in Title 23 of the California Code of Regulations. The San Joaquin River is listed in Table 8.1 and the proposed action could have an effect on the flood control functions of project levees just east and north of the Chowchilla Bifurcation Structure or downstream project levees. Therefore, an encroachment permit from the CVFPB (formerly known as the Reclamation Board) will likely be required for the proposed action. Approval by local reclamation districts may also be necessary.
Permit Purpose and Requirements The CVFPB issues encroachment permits to maintain the integrity and safety of flood control project levees and floodways that were constructed according to the flood control plans adopted by the CVFPB or the California Legislature.
The CVFPB has jurisdiction over the levee section, the waterward area between project levees, a 10-foot-wide strip adjacent to the landward levee toe, within 30 feet of the top of the banks of unleveed project channels, and within designated floodways adopted by the CVFPB. Activities outside of these limits that could adversely affect the flood control project also fall under the jurisdiction of the CVFPB.
5.2.6 California Water Rights
Application to Proposed Action The SJRRP is coordinating with the SWRCB to amend water rights at the Program level; however, those negotiations do not require action on the Project level. Most or all of the water rights present within the Project area are not under jurisdiction of the SWRCB because they are pre-1914 or riparian water rights. Therefore, it is unlikely that the Project will require coordination with the SWRCB. If water rights under the jurisdiction of the SWRCB are present, and if the Project required that the diversion point for the water rights be changed, it is possible that those water rights would have to be amended.
Permit Purpose and Requirements A water right is a legally protected right, granted by law, to take possession of water and put it to beneficial use. Under the California Water Code, SWRCB is responsible for
Mendota Pool Bypass and Reach 2B Improvements Project 5-14 – October 2012 Project Description Technical Memorandum 5.0 Project Implementation allocating surface water rights and permitting the diversion and use of water throughout the State. Through its Division of Water Rights, SWRCB issues permits to divert water for new appropriations or to change existing water rights. SWRCB attaches conditions to these permits to ensure that the water user prevents waste, conserves water, does not infringe on the rights of others, and puts the State’s water resources to the most beneficial
An applicant, permittee, or licensee who wishes to change the point of diversion, place of use, or purpose of use from that specified in an existing permit or license must petition SWRCB to amend a water right. When considering a petition for a water right amendment, SWRCB considers the same factors as those it considers when a water user applies for a new permit, such as waste prevention, water conservation, infringement on the rights of others, and public trust values.
5.2.7 State Lands Commission Land Use Lease
Application to Proposed Action The proposed action may directly affect lands, such as the San Joaquin River, under the jurisdiction of the SLC. The proposed action will therefore likely require a State lands lease agreement.
Permit Purpose and Requirements The SLC was given authority and responsibility to manage and protect the important natural and cultural resources on certain public lands within the State and public’s rights to access these lands. The public lands under the SLC’s jurisdiction are of two distinct types—sovereign and school lands. Sovereign lands encompass approximately 4 million acres. These lands include the beds of California’s naturally navigable rivers, lakes, and streams, as well as the State’s tidal and submerged lands along the coastline.
5.3 Local Actions
5.3.1 San Joaquin Valley Air Pollution Control District Regulations
Application to Proposed Action The Federal Clean Air Act (CAA) establishes national ambient air quality standards. Under the CAA, the U.S. EPA is responsible for setting and enforcing the Federal ambient air quality standards for atmospheric pollutants. Most regulatory responsibilities under the CAA are delegated to State, regional, or local government bodies. For the Project, the SJVAPCD has the authority to issue permits an ensure compliance with air quality regulations.
Any Federal agency providing financial assistance, issuing a license or permit, or approving or supporting in any way a proposed project located in a nonattainment or maintenance area for a criteria air pollutant is required to issue a conformity analysis. The conformity analysis must certify that the Federally permitted project is consistent with the State Implementation Plan (SIP) developed pursuant to the CAA. A conformity analysis is required unless the proposed action’s emissions are below the Federally established de
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minimis emissions thresholds, and the proposed action’s emissions do not reach the level of 10 percent or more of the regional emissions budget for any given pollutant in the nonattainment area. This is also applicable to short-term, construction-related emissions, and therefore applies to the Project.
The SJVAPCD is required by the California Clean Air Act (CCAA) to develop "indirect source" control programs in their attainment plans. The SJVAPCD committed to reducing PM10 and nitrous oxides emissions from indirect sources in the 2003 PM10 Plan and the 2004 Extreme Ozone Attainment Demonstration Plan. The SJVAPCD’s Governing Board adopted District Rule 9510 as a result of this commitment. To comply with this rule, the Project will have to submit an Air Impact Assessment (AIA) to the SJVAPCD.
Since the Project will not require the construction or operation of a major stationary source that is adding new emissions units or modifying existing emissions units, the Project will not require Construction or Operation Permits from the SJVAPCD. However, if the Project requires the use of equipment (i.e., a generator) with an internal combustion engine with a rated brake horsepower greater than 50 horsepower that will operate less than six months at one location, a Portable Equipment Certification from SJVAPCD will be necessary.
Finally, because the proposed action would likely involve the construction of a nonresidential development of more than 5 acres of disturbed surface area and could involve moving, depositing, or relocating more than 2,500 cubic yards per day of bulk materials on at least 3 days, a Dust Control Plan is required by SJVAPCD.
Permit Purpose and Requirements The CAA requires areas with unhealthy levels of ozone, carbon monoxide, nitrogen dioxide, sulfur dioxide, and inhalable particulate matter to develop SIPs to comply with the national ambient air quality standards (42 USC §7410 et seq.). Federal agencies must conform to SIPs, meaning they must ensure that Federally supported activities will not cause or contribute to a new violation, increase the severity of an existing violation, or delay timely attainment of any standard in any area (42 USC §7506(c)(1)(B)).
A Federal action conforms with the applicable SIP if: (1) the total of direct and indirect emissions from the action are compliant and consistent with the requirements of the SIP, and (2) one of a list of enumerated, pollutant-specific requirements are satisfied (such as accounting for the Federal action’s projected emission of any criteria pollutant in the SIP, or offsetting ozone or nitrogen dioxide emissions within the nonattainment area) (42 CFR §93.158(a)). Ultimately, a conformity analysis may require revising the SIP, implementing mitigation measures to bring the Federal action’s emissions levels down, or altering the Project to reduce emissions to levels within the budgets established by the SIP for specific pollutants.
In accordance with SJVAPCD Rule 9510 Indirect Source Review (ISR), applicants must mitigate project impacts through the incorporation of on-site emission reducing design elements and/or the payment of fees that would be used to fund off-site emissions
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reduction projects. Applicants subject to the rule must submit an AIA application to the SJVFCD no later than when applying for final discretionary approval, and must pay any applicable off-site mitigation fees before issuance of the first grading/building permit.
In accordance with SJVAPCD Rule 2020 – Exemptions – emissions units that qualify and are registered as Portable Equipment do not require Construction and Operating Permits. If the Project requires the use of an internal combustion engine with a rated brake horsepower greater than 50 horsepower to operate for less than six months, it must be registered as Portable Equipment to be exempt from requirements under Rule 4702 – Internal Combustion Engines.
In accordance with SJVAPCD Rule 8021 – Construction, Demolition, Excavation, Extraction, and Other Earthmoving Activities, the owner or operator of a construction project is required to submit a Dust Control Plan to SJVAPCD if at any time the project would involve:
• residential developments of 10 or more acres of disturbed surface area; • nonresidential developments of 5 or more acres of disturbed surface area; or • moving, depositing, or relocating of more than 2,500 cubic yards per day of bulk materials on at least three days of the project A Dust Control Plan identifies the fugitive dust sources at the construction site and describes all of the dust control measures to be implemented before, during, and after any dust-generating activity for the duration of the project. SJVAPCD will review and make a determination on the Dust Control Plan. Construction activities shall not commence until the Dust Control Plan has been approved or conditionally approved.
At least one key individual representing the owner or operator, or any person who prepares a Dust Control Plan, must complete a Dust Control Training Course presented by SJVAPCD. SJVAPCD will be contacted to determine when courses are offered. For those who need to submit a Dust Control Plan but have not had the course, SJVAPCD will accept the Dust Control Plan with the contingency that the individual sign up for the next scheduled course.
Regardless of whether an SJVAPCD-approved Dust Control Plan is in place, the owner or operator is required to comply with all requirements of the applicable rules under Regulation VIII and SJVAPCD’s Rules and Regulations at all times.
5.3.2 Surface Mining and Reclamation Act of 1975
Application to Proposed Action The requirements of the Surface Mining and Reclamation Act of 1975 (SMARA) apply to anyone, including government agencies, engaged in surface mining operations in California (including those on Federally managed lands) that disturb more than one acre or remove more than 1,000 cubic yards of material. This includes, but is not limited to, prospecting and exploratory activities, dredging and quarrying, streambed skimming, borrow pitting, and the stockpiling of mined materials.
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SMARA does not typically apply to on-site excavation and on-site earthmoving activities that are an integral and necessary part of a construction project and that are undertaken to prepare a site for construction of structures, landscaping or other land improvements, including the related excavation, grading, compaction or the creation of fills, road cuts and embankments. This is true whether or not surplus materials are exported from the site so long as required permits are approved by public agencies, the county’s approval included consideration of the on-site excavation and on-site earthmoving activities pursuant to CEQA, the project is consistent with the general plan or zoning of the site, and surplus materials are not exported from the site until actual construction work has commenced and cease when construction activities have terminated. However, the SMARA process may be required, as determined by the county, for earth-moving projects that exceed 1,000 cubic yards if greater than 80 percent of the material is disposed of offsite.
Permit Purpose and Requirements The SMARA (Public Resources Code, Sections 2710-2796) provides a comprehensive surface mining and reclamation policy with the regulation of surface mining operations to assure that adverse environmental impacts are minimized and mined lands are reclaimed to a usable condition. SMARA also encourages the production, conservation, and protection of the State’s mineral resources. On a State level, the Department of Conservation’s Office of Mine Reclamation and the State Mining and Geology Board are jointly charged with ensuring proper administration of the SMARA’s requirements.
City and county lead agencies adopt ordinances for land use permitting and reclamation procedures that provide the regulatory framework under which local mining and reclamation activities are conducted. SMARA lead agencies review applications for permits and/or reclamation plans (or amendments thereto), submit reclamation plans and financial assurances to the State for technical review and comment prior to approval, annually review financial assurances, annually inspect mining operations for compliance, and take enforcement actions where necessary.
Financial assurances are required to ensure compliance with elements of the reclamation plan, including but not limited to revegetation and landscaping requirements, restoration of aquatic or wildlife habitat, restoration of water bodies and water quality, slope stability and erosion and drainage control, disposal of hazardous materials, and other measures, if necessary.
5.3.3 Williamson Act
Application to Proposed Action Land within the Project area may be under a Williamson Act contract.
Permit Purpose and Requirements The California Land Conservation Act (Government Code §51200 et seq.) of 1965, commonly known as the Williamson Act, provides a tax incentive for the voluntary enrollment of agricultural and open space lands in contracts between local government and landowners. The contract restricts the land to agricultural and open space uses and
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compatible uses defined in state law and local ordinances. Local government establishes an agricultural preserve defining the boundary within which a city or county will enter into contracts with landowners. Local governments calculate the property tax assessment based on the actual land use instead of the potential land value assuming full development.
Williamson Act contracts are for 10 years and longer. The contract is renewed automatically each year, maintaining a constant, 10-year contract, unless the landowner or local government files to initiate nonrenewal. Should that occur, the Williamson Act would terminate 9 years after the filing of a notice of nonrenewal. Only a landowner can petition for a contract cancellation. Tentative contract cancellations can be approved only by a local government. The cancellation fee typically must be paid by the landowner.
California Government Code (§51290–51295) outlines the procedure for locating a public use on Williamson Act contracted land, which may apply to the Project and is described in the following section.
5.4 Applicable Laws, Policies, and Plans Not Requiring Specific Permit or Approval
5.4.1 Federal
Migratory Bird Treaty Act The Migratory Bird Treaty Act (MBTA), first enacted in 1918, implements domestically a series of treaties between the United States and Great Britain (on behalf of Canada), Mexico, Japan, and the former Soviet Union that provide for international migratory bird protection. The MBTA authorizes the Secretary of the Interior to regulate the taking of migratory birds; the act provides that it shall be unlawful, except as permitted by regulations, “to pursue, take, or kill any migratory bird, or any part, nest or egg of any such bird…” (USC Title 16, Section 703). This prohibition includes both direct and indirect acts, although harassment and habitat modification are not included unless they result in direct loss of birds, nests, or eggs. The current list of species protected by MBTA includes several hundred species and essentially includes all native birds. The act offers no statutory or regulatory mechanism for obtaining an incidental take permit for the loss of nongame migratory birds.
Bald and Golden Eagle Protection Act The Bald Eagle Protection Act (16 USC 668 668d, 54 Stat. 250) as amended, provides protection for the bald eagle (Haliaeetus leucocephalus) and golden eagle (Aquila chrysaetos) by prohibiting the taking, possession, and commerce of such birds, their nests, eggs, or feathers unless expressly authorized by permit pursuant to Federal regulations.
Executive Order 11990 (Wetlands Policy) Executive Order 11990 is an overall wetlands policy for all agencies that manage Federal lands, sponsor Federal projects, or provide Federal funds to State or local projects. The
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order requires Federal agencies to follow avoidance, mitigation, and preservation procedures with public input before they propose new construction in wetlands. Executive Order 11990 can restrict the sale of Federal land containing wetlands; however, it does not apply to Federal discretionary authority for non-Federal projects (other than funding) on non-Federal land.
Before implementing an action that is located in a wetland or may affect a wetland, Federal agencies must demonstrate that there is no practical alternative and that the proposed action includes all practical measures to minimize harm to the wetlands. To demonstrate compliance with Executive Order 11990, Reclamation must make such a demonstration if appropriate, provide the opportunity for early public review, and disclose its findings in the Project EIS/R and/or subsequent NEPA documents.
Projects requiring compliance with Executive Order 11990 (except USACE projects) are likely to require a permit under CWA Section 404. The assessment of effects of the proposed action on wetlands should be closely coordinated with the Section 404 process.
Executive Order 11988 (Flood Hazard Policy) Executive Order 11988 is a flood hazard policy for all Federal agencies that manage Federal lands, sponsor Federal projects, or provide Federal funds to State or local projects. It requires that all Federal agencies take necessary action to reduce the risk of flood loss; restore and preserve the natural and beneficial values served by floodplains; and minimize the impacts of floods on human safety, health, and welfare. Specifically, Executive Order 11988 dictates that all Federal agencies avoid construction or management practices that would adversely affect floodplains unless that agency finds that there is no practical alternative and the proposed action has been designed or modified to minimize harm to or within the floodplain.
Before implementing a proposed action, Federal agencies are required to determine whether the action would occur in a floodplain. This determination must be made according to a floodplain map provided by the Department of Housing and Urban Development or, if available, a more detailed map of an area. If the Federal agency proposes an action in a floodplain, it must consider alternatives to avoid adverse effects and incompatible development in the floodplain. If the agency finds that the only practicable alternative requires that the project be sited in a floodplain, it must:
• design or modify its action to minimize potential harm to or within the floodplain • prepare and circulate a notice, not to exceed three pages in length, that includes: - reasons why the action is proposed to be located in a floodplain - a statement indicating whether the action conforms to applicable State or local floodplain protection standards - a list of alternatives considered The agency should send the notice to the State Clearinghouse.
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To demonstrate compliance, Reclamation must conduct this determination and consider alternatives as appropriate, provide an opportunity for early public review by those who may be affected, and disclose its findings in the NEPA documentation.
Executive Order 12898 (Environmental Justice Policy) Executive Order 12898 requires Federal agencies to identify and address disproportionately high and adverse human health and environmental effects of Federal programs, policies, and activities on minority and low-income populations. These effects are to be considered in terms of both their frequency and magnitude. Executive Order 12898 requirements apply to all Federal actions that are located on Federal lands, sponsored by a Federal agency, or funded with Federal monies and may affect minority or low-income populations. This executive order was incorporated into California State Government through California Government Code, Section 65040.12, which codified a definition of environmental justice and established the Governor’s Office of Planning and Research as the coordinating agency in state government for environmental justice programs.
To demonstrate compliance with Executive Order 12898, the lead agency must show that it has considered the effects of the proposed action on minority and low-income populations and must design the proposed action to ensure that the action does not result, either directly or indirectly, in discrimination on the basis of race, color, or national origin.
There is no single analytical approach to environmental justice analysis, but the approach chosen should be designed to incorporate any unique circumstances of the community potentially affected by a proposed project. The use of multiple approaches in this analysis is encouraged to ensure the accuracy and completeness of findings. In all cases, the agency must undertake specific outreach to any identified minority and low-income populations. This outreach is to be specifically targeted to allow environmental justice populations to fully participate in the public involvement process. The agency must also provide an opportunity for early public review by those who may be affected, and must include a description of the specific outreach undertaken and all findings in the Project EIS/R. If a proposed Federal action will not result in significant adverse impacts on minority and low-income populations, the Project EIS/R must describe how Executive Order 12898 was addressed during the NEPA process.
Executive Order 13112 (Invasive Species) Executive Order 13112 requires Federal agencies to perform measures to minimize the spread of invasive species and to reintroduce native species where possible. This order applies to “actions [that] may affect the status of invasive species” (§2). Federal agencies must pursue the duties mandated under the order in consultation with the Invasive Species Council (§2(b)). The order also requires agencies to formulate their own Invasive Species Management Plan (ISMP) (§5). Restoration activities and planning will be integrated with Reclamation’s ISMP. The following list will be key species to be evaluated and have been observed in the Project area:
• tree tobacco (Nicotiana glauca)
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• giant reed grass (Arundo donax) • tamarisk (Tamarix sp.) • perennial pepperweed (Lepidium latifolium) • yellow star thistle (Centaurea solstitialis) • Italian thistle (Carduus pycnocephalus) • ripgut brome (Bromus diandrus) • Bermuda grass (Cynodon dactylon) • prickly lettuce (Lactuca serriola) • Russian knapweed (Rhaponticum repens) • rabbitsfoot grass (Polypogon monspeliensis)
Executive Order 13186 (Migratory Birds) Executive Order 13186 directs Federal agencies to take certain actions to further implement the MBTA and outlines the responsibilities of Federal agencies to protect migratory birds. Specifically, this order directs Federal agencies with direct activities that will likely result in the take of migratory birds, to develop and implement an MOU with the USFWS that shall promote the conservation of migratory bird populations, with emphasis on species of concern. Reclamation has not finalized the MOU required in this order pending Department of Interior guidance. Reclamation has begun implementing the conservation measures set forth in this order, however, as appropriate and applicable.
Birds protected under the MBTA include all common songbirds, waterfowl, shorebirds, hawks, owls, eagles, ravens, crows, native doves and pigeons, swifts, martins, swallows, and others, including their body parts (feathers, plumes, etc.), nests, and eggs. A complete list of protected species is found at 50 CFR 10.13. Project activities that are most likely to result in take of migratory birds include, but are not limited to, clearing or grubbing of migratory bird nesting habitat during the nesting season when eggs or young are likely to be present. Efforts will be made to remove nesting habitat or inactive nests of migratory birds outside of the bird breeding season, and such activities will occur in coordination with the USFWS office with local jurisdiction.
Executive Order 13007 (Indian Sacred Sites) Executive Order 13007 requires Federal land management agencies to “accommodate access to and ceremonial use of Indian sacred sites by Indian religious practitioners and avoid adversely affecting the physical integrity of such sacred sites.” Additionally, the order requires Federal agencies to provide notice of proposed actions or land management policies that may restrict future access to or ceremonial use of, or adversely affect the physical integrity of, sacred sites. If an Indian sacred site is encountered within the Project area, measures will be implemented to prevent any restriction of access or effect on the site’s physical integrity.
Indian Trust Assets All Federal agencies have a responsibility to protect Indian Trust Assets. Indian Trust Assets are legal interests in assets held in trust by the Federal government for Native
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American tribes or individuals. Assets may be owned property, physical assets, intangible property rights, a lease, or the right to use something and typically include lands, minerals, water rights, hunting and fishing rights, natural resources, money, and claims. If Indian Trust Assets may be affected by the proposed action, mitigation or compensation measures are to be identified so that no net loss is incurred by the Native American beneficial owners of the asset.
Farmland Protection Policy Act The Farmland Protection Policy Act requires that a Federal agency examine the potential impacts of a proposed action on prime and unique farmland, as defined by the Natural Resources Conservation Service (NRCS), and if the action would adversely affect farmland preservation, consider alternatives to lessen the adverse effects. As a Federal agency preparing an EIS, Reclamation is required to include in its analysis a farmland assessment designed to minimize adverse impacts on prime and unique farmlands and provide for mitigation as appropriate. Compliance with the Farmland Protection Policy Act could include early consultation and coordination with NRCS.
Native American Graves Protection and Repatriation Act The Native American Graves Protection and Repatriation Act (25 USC Sections 3001 to 3013) sets provisions for the removal and inadvertent discovery of human remains and other cultural items on Federal and tribal lands. The Native American Graves Protection and Repatriation Act clarifies the ownership of human remains and sets forth a process for repatriation of human remains and associated funerary objects and sacred religious objects to the Native American tribes or tribes likely to be lineal descendants or culturally affiliated with the discovered remains or objects.
5.4.2 State
California Native Plant Protection Act Sections 1900 1913 of the Fish and Game Code (California Native Plant Protection Act of 1977) establish criteria for the preservation, protection, and enhancement of endangered or rare native plants of the State. The California Native Plant Protection Act protects endangered and rare species, subspecies, and varieties of wild plants native to California. This act requires all State agencies to use their authority to carry out programs to conserve endangered and rare native plants. Provisions of the California Native Plant Protection Act prohibit the taking of listed plants from the wild and require notification of the DFG at least 10 days in advance of any change in land use. This allows the DFG to salvage listed plant species that would otherwise be destroyed. The project sponsor is required to conduct botanical inventories and consult with the DFG during project planning to comply with the provisions of this act and sections of CEQA that apply to rare or endangered plants.
California Native Plant Society Species Designations The California Native Plant Society (CNPS) is a statewide nonprofit organization that seeks to increase understanding of California’s native flora and to preserve this rich resource for future generations. CNPS has developed and maintains lists of vascular plants of special concern in California. CNPS-listed species have no formal legal
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protection, but the values and importance of these lists are widely recognized. CNPS List 1 and 2 species are considered rare plants pursuant to Section 15380 of CEQA, and it is recommended that they be fully considered while preparing environmental documents relating to CEQA.
Porter-Cologne Water Quality Control Act Under the Porter-Cologne Water Quality Control Act, the RWQCBs have jurisdiction over State water quality permitting activities. The Porter-Cologne Water Quality Control Act specifies water quality provisions and discharge requirements for regulating the discharge of waste that could affect the quality of waters of the State. Under the act, the SWRCB has the ultimate authority over State water rights and water quality policy. However, the appropriate RWQCB is tasked with setting waste discharge requirements for projects and for updating basin plans (water quality control plans) for protected waters of the State. Waters of the State are defined as “any surface water or groundwater, including saline waters, within the boundaries of the State (Water Code section 13050(e)) which include all waters within the State’s boundaries, whether private or public, including waters in both natural and artificial channels.”
Under the act, RWQCB must prepare and periodically update water quality control basin plans. Each basin plan sets forth water quality standards for surface water and groundwater, as well as actions to control nonpoint and point sources of pollution to achieve and maintain these standards. Projects that affect wetlands or waters must meet RWQCB waste discharge requirements, which may be issued in addition to a water quality certification under Section 401 of the CWA.
California Register of Historical Resources Public Resources Code Section 5024.1 establishes the California Register of Historical Resources (CRHR). The register lists all properties considered to be significant historical resources in the State. The CRHR includes all properties listed or determined eligible for listing on the NRHP, including properties evaluated under Section 106. The criteria for listing are similar as those of the NRHP. CEQA (Public Resources Code) Section 21084.1 requires a finding of significance for substantial adverse changes to historical resources and defines the term “historical resources.” CEQA Section 21083.2 and CEQA Guidelines Section 15064.5(c) provide further definitions and guidance for archaeological sites and their treatment. The lead agency is required to follow the established guidelines during the CEQA process.
California Native American Graves Protection and Repatriation Act The California Native American Graves Protection and Repatriation Act (California Health & Safety Code Section 8010 et seq.) establishes a State repatriation policy intent that is consistent with and facilitates implementation of the Federal Native American Graves Protection and Repatriation Act. The act strives to ensure that all California Indian human remains and cultural items are treated with dignity and respect, and states an intent for the State to provide mechanisms for aiding California Indian tribes, including non-Federally recognized tribes.
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5.4.3 Local The counties of Fresno and Madera, and their respective public works departments, will require compliance with local plans and ordinances, such as County general plans, zoning ordinances, grading plan, and various use permits. Specifically, although neither county has ordinances requiring tree protection, both counties have provided voluntary guidelines for the protection of oaks and heritage trees.
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6.0 Acknowledgments The preparers would like to acknowledge the input and participation of Bureau of Reclamation and other SJRRP staff, third-party consultants, resource agency staff, and others. A partial list of these participants includes:
Michelle Banonis Reclamation Bob Mussetter Tetra Tech Lisa Fotherby Reclamation Nick Hindman USFWS Alicia Gasdick Reclamation Zac Jackson USFWS Elaina Gordon Reclamation Becky Lorig USFWS Blair Greimann Reclamation Carl Mesick USFWS Katrina Harrison Reclamation Donnie Ratcliff USFWS Jeremy Lorberau Reclamation Stephanie Rickabaugh USFWS David Mooney Reclamation Kim Webb USFWS Erin Rice Reclamation Michelle Workman USFWS Karen Dulik DWR Larry Brown USGS David Encinas DWR Steven Phillips USGS Greg Farley DWR George Heise DFG Alexis Phillips-Dowell DWR Dale Stanton DFG Paul Romero DWR Leslie Mirise NMFS Susan Cundiff Tetra Tech Erin Strange NMFS Chad Morris Tetra Tech Steve Thomas NMFS
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7.0 References Barbour 2007. Barbour, M.G., T. Keeler-Wolf, and A. Schoenherr. Terrestrial Vegetation of California. Third Edition.
CDF 2007. California Department of Finance. Population Projections for California and Its Counties 2000-2050 by Age, Gender and Race/Ethnicity. Sacramento. July.
CVFED 2009. Central Valley Floodplain Evaluation and Delineation and San Joaquin River Restoration Program LiDAR data and aerial imagery. Produced for California Department of Water Resources. April 9.
DFG 1998. California Department of Fish and Game. California Salmonid Stream Habitat Restoration Manual, Third Edition. January.
DWR 2009a. California Department of Water Resources. Chowchilla Bifurcation Structure Gate Seal Installation Notice of Exemption. August.
DWR 2009b. California Department of Water Resources. Draft San Joaquin River Restoration Program Geotechnical Investigation and Seepage Well Installation Project Initial Study/Mitigated Negative Declaration. October.
DWR 2009c. California Department of Water Resources. San Joaquin River Restoration Program Scour Chain Installation and Data Collection Notice of Exemption. February.
DWR 2009d. California Department of Water Resources. San Joaquin River Restoration Program Stream Bed and Sand Sampling Notice of Exemption. April.
DWR 2009e. California Department of Water Resources. San Joaquin River Restoration Program Stream Gage Installation and Operation and Maintenance Project Initial Study/Mitigated Negative Declaration. March.
DWR 2009f. California Department of Water Resources. San Joaquin River Restoration Program Water Level Recorder Installation and Data Collection Notice of Exemption. February.
Grosholz 2006. Grosholz, Edwin and E. Gallo 2006. The influence of flood cycle and fish predation on invertebrate production on a restored California floodplain. Hydrobiologia. (2006) 568: 91-109.
Houk, 2009. Randy Houk. Personal communication with the Reach 2B team during a site visit. December 15.
Mendota Pool Bypass and Reach 2B Improvements Project Project Description Technical Memorandum 7-1 – October 2012 San Joaquin River Restoration Program
Jeffres 2008. Jeffres, Carson A., J.J. Opperman and P. B. Moyle. Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California River. Environmental Biology of Fishes. Vol. 83, No. 4. Pages 449- 458.
McBain & Trush 2002. San Joaquin River Restoration Study Background Report. Prepared by Friant Water Users Authority, Lindsay, California, and Natural Resources Defense Council, San Francisco, California. December.
NMFS 2001. National Marine Fisheries Service, Southwest Region. Guidelines for Salmonid Passage at Stream Crossings. September.
NMFS 2008. National Marine Fisheries Service, Northwest Region. Anadromous Salmonid Passage Facility Design. February.
Pacific States Marine Fisheries Commission 2007. CalFish Passage Assessment Database. Downloaded from www.calfish.org.
Reclamation 2006. U.S. Bureau of Reclamation. Water Resources Technical Publication, Fish Protection at Water Diversions, a Guide for Planning and Designing Fish Exclusion Facilities. April.
Reclamation 2008. U.S. Bureau of Reclamation. Installation and Rehabilitation of Stream Gages on the San Joaquin River, Fresno, Madera, and Merced Counties, California Environmental Assessment/Finding of No Significant Impact. December.
Reclamation 2010. U.S. Bureau of Reclamation. Water Year 2011 Interim Flows Project Supplemental Environmental Assessment and Finding of No Significant Impact. September.
Reclamation and DWR 2009. U.S. Bureau of Reclamation and California Department of Water Resources. San Joaquin River Restoration Program Water Year 2010 Interim Flows Project, Environmental Assessment and Finding of No Significant Impact/Initial Study and Mitigated Negative Declaration. October.
SJRRP 2010a. San Joaquin River Restoration Program. Draft Mendota Pool Bypass and Reach 2B Improvements Project Technical Memorandum on Environmental Field Survey Results. November.
SJRRP 2010b. San Joaquin River Restoration Program. First Administrative Draft Mendota Pool Bypass and Reach 2B Project Technical Memorandum on Regulatory Compliance. December.
SJRRP 2010c. San Joaquin River Restoration Program. Mendota Pool Bypass and Reach 2B Improvements Project Public Scoping Report. February.
Mendota Pool Bypass and Reach 2B Improvements Project 7-2 – October 2012 Project Description Technical Memorandum 7.0 References
SJRRP 2010d. San Joaquin River Restoration Program. Mendota Pool Bypass and Reach 2B Improvements Project Technical Memorandum on Initial Options. April.
SJRRP 2010e. San Joaquin River Restoration Program. Mendota Pool Bypass and Reach 2B Improvements Project Technical Memorandum on Selection and Use of Analytical Tools. October.
SJRRP 2011. San Joaquin River Restoration Program. Draft San Joaquin River Restoration Program PEIS/R. April.
SJRRP 2012. San Joaquin River Restoration Program. Third Party Working Draft Framework for Implementation. June 19.
Sommer 2001. Sommer, T.R., M.L. Nobriga, W.C. Harrell, W. Batham and W.J. Kimmerer. Floodplain rearing of juvenile Chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences. Volume 58. Pages 325–333
Sommer 2004. Sommer, T. R., W.C. Harrell, A.M. Solger, B. Tom and W. Kimmerer. Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River, California, USA. Aquatic Conservation-Marine and Freshwater Ecosystems. Volume 14. Pages 247–261.
Tetra Tech 2011a. Fresno Slough Dam Alternative - Elimination of Mendota Dam Option. September 22.
Tetra Tech 2011b. Mendota Pool Bypass Final Alternatives - Mendota Bypass Channel with no Grade-control Option. November 16.
Tetra Tech 2012. Reach 2B Floodplain Alternatives Supplemental Analysis. January 9.
USACE 2000a. U.S. Army Corps of Engineers. Engineer Manual 1110-2-1313 Design and Construction of Levees. April 30.
USACE 2000b. U.S. Army Corps of Engineers. Engineer Manual 1110-2-301 Guidelines for Landscape Planting and Vegetation Management at Floodwalls, Levees, & Embankment Dams. January 1.
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Mendota Pool Bypass and Reach 2B Improvements Project
Project Description Technical Memorandum Attachment A – Initial Alternatives Evaluation
October 2012
1 Table of Contents
2 1.0 Introduction ...... 1-1 3 1.1 Purpose of this Attachment ...... 1-1 4 1.2 Summary of the Alternatives Formulation Process ...... 1-1 5 1.3 Initial Alternatives Evaluation Process and Methods ...... 1-3 6 1.4 Organization of this Attachment ...... 1-4
7 2.0 Opportunities and Constraints ...... 2-1 8 2.1 Opportunities ...... 2-1 9 2.1.1 Habitat Improvement for Other Native and Special Status 10 Species ...... 2-1 11 2.1.2 Open Space & Mitigation ...... 2-2 12 2.1.3 Recreation ...... 2-2 13 2.1.4 Water Quality ...... 2-3 14 2.1.5 Education ...... 2-3 15 2.1.6 Flood System ...... 2-4 16 2.2 Constraints ...... 2-4 17 2.2.1 Settlement and Act Requirements ...... 2-4 18 2.2.2 Other Legal and Regulatory Compliance ...... 2-4 19 2.2.3 Operations for Flood Releases and Water Deliveries ...... 2-5 20 2.2.4 Fish Passage ...... 2-7 21 2.2.5 Special Status Species ...... 2-8 22 2.2.6 Cultural and Historical Resources ...... 2-8 23 2.2.7 Land Use/Agriculture and Socioeconomic/Environmental 24 Justice ...... 2-8 25 2.2.8 Seepage ...... 2-9 26 2.2.9 River Crossings ...... 2-9 27 2.2.10 Geomorphology ...... 2-9 28 2.2.11 Recreation ...... 2-10 29 2.2.12 Illegal Dumping ...... 2-11 30 2.2.13 Sand Mining ...... 2-11
31 3.0 Goals and Objectives ...... 3-1 32 3.1 Flow Conveyance ...... 3-1 33 3.2 Water Supply ...... 3-3 34 3.3 Fish Habitat and Passage ...... 3-4 35 3.3.1 Fish Habitat Goals and Objectives ...... 3-5
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation i – October 2012 San Joaquin River Restoration Program
1 3.3.2 Fish Passage Goals and Objectives ...... 3-6 2 3.4 Habitat Restoration ...... 3-8 3 3.5 Seepage ...... 3-9 4 3.6 Geomorphology ...... 3-10
5 4.0 Pre-Initial Options Analysis ...... 4-1
6 5.0 Initial Options Refinement ...... 5-1 7 5.1 Pre-Evaluation Screening ...... 5-1 8 5.1.1 Bottomless Arch Culverts ...... 5-1 9 5.1.2 Corrugated Metal Pipe Culverts...... 5-1 10 5.1.3 Bridge ...... 5-1 11 5.1.4 San Mateo Avenue Crossing Removal ...... 5-1 12 5.1.5 Floodplain Vegetation Types ...... 5-1 13 5.1.6 Floodplain Recontouring ...... 5-2 14 5.1.7 Older Levee Setbacks ...... 5-2 15 5.1.8 Mendota Dam Removal ...... 5-2 16 5.1.9 Channel Grading from Reach 3 to Chowchilla Bifurcation 17 Structure ...... 5-2 18 5.1.10 Floating Picket Weir ...... 5-3 19 5.1.11 Behavioral Barrier ...... 5-3 20 5.1.12 Velocity Barrier ...... 5-4 21 5.1.13 Other Types of Fish Screens ...... 5-4 22 5.1.14 Pump Diversion to Mendota Pool ...... 5-4 23 5.2 Other Refinements ...... 5-5 24 5.2.1 Levee Alignments ...... 5-5 25 5.2.2 Floodplain Grading ...... 5-5 26 5.2.3 Removal of Existing Levees ...... 5-5 27 5.2.4 Placement of Structures ...... 5-6 28 5.2.5 Operational Flexibility ...... 5-6 29 5.2.6 Fish Passage Design Criteria ...... 5-6 30 5.2.7 Columbia Canal Relocation Facilities ...... 5-7 31 5.2.8 Fresno Slough Dam Height ...... 5-8 32 5.2.9 Picket Barriers ...... 5-9 33 5.2.10 Infrastructure Relocations and Floodproofing ...... 5-9 34 5.2.11 Seepage Mitigation ...... 5-9
35 6.0 Initial Alternatives Evaluation Criteria ...... 6-1 36 6.1 Implementation/Technical Feasibility ...... 6-1
Mendota Pool Bypass and Reach 2B Improvements Project ii – October 2012 Attachment A – Initial Alternatives Evaluation Table of Contents
1 6.1.1 Costs ...... 6-1 2 6.1.2 Time to Build ...... 6-4 3 6.2 Objectives/Benefits Achievement ...... 6-4 4 6.2.1 Flow Conveyance...... 6-4 5 6.2.2 Fish Habitat and Passage ...... 6-4 6 6.2.3 Habitat Restoration ...... 6-11 7 6.2.4 Geomorphology ...... 6-13 8 6.3 Preliminary Impact Assessment ...... 6-14 9 6.3.1 Groundwater ...... 6-14 10 6.3.2 Land Use ...... 6-15 11 6.3.3 Socioeconomics and Economics ...... 6-15 12 6.3.4 Environmental ...... 6-17 13 6.4 Scoring Alternatives Data and Professional Judgment ...... 6-21
14 7.0 Initial Alternatives Descriptions ...... 7-1 15 7.1 Floodplain Initial Alternatives ...... 7-1 16 7.1.1 Elements Common to All Floodplain Initial Alternatives ...... 7-3 17 7.1.2 FP-1 ...... 7-10 18 7.1.3 FP-2 ...... 7-14 19 7.1.4 FP-3 ...... 7-18 20 7.1.5 FP-4 ...... 7-22 21 7.1.6 FP-5 ...... 7-26 22 7.2 Bypass Initial Alternatives ...... 7-30 23 7.2.1 Elements Common to All Bypass Initial Alternatives ...... 7-30 24 7.2.2 Settlement Alignment ...... 7-31 25 7.2.3 Compact Alignment ...... 7-37 26 7.2.4 Fresno Slough Dam...... 7-44 27 7.3 Structures Included in the Initial Alternatives ...... 7-50 28 7.3.1 Chowchilla Bifurcation Structure Fish Passage Retrofit ...... 7-50 29 7.3.2 Lone Willow Slough Fish Screen ...... 7-51 30 7.3.3 San Mateo Avenue Crossing ...... 7-51 31 7.3.4 Mendota Pool Bypass Bifurcation Structure...... 7-51 32 7.3.5 Mendota Pool Bypass Fish Ladder ...... 7-52 33 7.3.6 Drive 10 ½ Crossing ...... 7-52 34 7.3.7 Mendota Pool Bypass Fish Screen ...... 7-52 35 7.3.8 Mendota Dam Fish Barrier ...... 7-53 36 7.3.9 Mendota Pool Bypass Channel Grade Control Structures ...... 7-53 37 7.3.10 Fresno Slough Dam...... 7-54
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation iii – October 2012 San Joaquin River Restoration Program
1 7.3.11 Mendota Dam Fish Passage Facilities ...... 7-54 2 7.3.12 Main Canal and Helm Ditch Relocations ...... 7-55 3 7.4 Project Options ...... 7-56 4 7.4.1 Bend 10 Revetment or Columbia Canal Relocation ...... 7-56 5 7.4.2 Water Delivery Canal Options ...... 7-57 6 7.4.3 7,000 cfs Capacity ...... 7-60
7 8.0 Initial Alternatives Evaluation Results ...... 8-1 8 8.1 Evaluation by Settlement Goals and Settlement Defined 9 Improvements ...... 8-1 10 8.2 Evaluation by Alternative ...... 8-3 11 8.2.1 FP-1 ...... 8-3 12 8.2.2 FP-2 ...... 8-3 13 8.2.3 FP-3 ...... 8-3 14 8.2.4 FP-4 ...... 8-4 15 8.2.5 FP-5 ...... 8-4 16 8.2.6 Settlement Alignment ...... 8-4 17 8.2.7 Compact Alignment ...... 8-4 18 8.2.8 Fresno Slough Dam...... 8-5 19 8.3 Comparisons of Initial Alternatives ...... 8-5 20 8.3.1 Based on Fish Habitat and Passage Criteria ...... 8-5 21 8.3.2 Based on Costs ...... 8-6 22 8.3.3 Based on Implementation/Technical Feasibility Perspective ...... 8-7 23 8.3.4 Based on Objectives/Benefits Achievement Perspective ...... 8-8 24 8.3.5 Based on Impacts Perspective ...... 8-8 25 8.3.6 Based on All Criteria ...... 8-9 26 8.4 Recommended Alternatives for Inclusion in the EIS/R Project 27 Description ...... 8-10 28 8.4.1 Alternatives Eliminated ...... 8-10 29 8.4.2 Alternatives Modified to Reduce Impacts ...... 8-12 30 8.5 Recommended Additional Analysis or Study...... 8-12
31 9.0 Acknowledgments ...... 9-1
32 10.0 References ...... 10-1 33
Mendota Pool Bypass and Reach 2B Improvements Project iv – October 2012 Attachment A – Initial Alternatives Evaluation Table of Contents
1 Tables
2 Table 2-1 Laws, Regulations, Executive Orders, and Policies ...... 2-5 3 Table 3-1 Restoration Area Habitat Goals and Compatible Reach 2B 4 Habitat Goals ...... 3-7 5 Table 5-1. Fish Design Criteria...... 5-7 6 Table 6-2. Wildlife habitat crosswalk ...... 6-12 7 Table 6-3. Buried deposits sensitivity according to landform age class ...... 6-21 8 Table 7-1. FP-1 Levees, Relocations, and Land Acquisition ...... 7-11 9 Table 7-2. FP-1 Implementation/Technical Feasibility Evaluation Data ...... 7-11 10 Table 7-3. FP-1 Objectives/Benefits Achievement Evaluation Data ...... 7-12 11 Table 7-4. FP-1 Impacts Evaluation Data ...... 7-13 12 Table 7-5. FP-2 Levees, Relocations, and Land Acquisition ...... 7-15 13 Table 7-6. FP-2 Implementation/Technical Feasibility Evaluation Data ...... 7-15 14 Table 7-7. FP-2 Objectives/Benefits Achievement Evaluation Data ...... 7-16 15 Table 7-8. FP-2 Impacts Evaluation Data ...... 7-17 16 Table 7-9. FP-3 Levees, Relocations, and Land Acquisition ...... 7-19 17 Table 7-10. FP-3 Implementation/Technical Feasibility Evaluation Data ...... 7-19 18 Table 7-11. FP-3 Objectives/Benefits Achievement Evaluation Data ...... 7-20 19 Table 7-12. FP-3 Impacts Evaluation Data ...... 7-21 20 Table 7-13. FP-4 Levees, Relocations, and Land Acquisition ...... 7-23 21 Table 7-14. FP-4 Implementation/Technical Feasibility Evaluation Data ...... 7-23 22 Table 7-15. FP-4 Objectives/Benefits Achievement Evaluation Data ...... 7-24 23 Table 7-16. FP-4 Impacts Evaluation Data ...... 7-25 24 Table 7-17. FP-5 Levees, Relocations, and Land Acquisition ...... 7-27 25 Table 7-18. FP-5 Implementation/Technical Feasibility Evaluation Data ...... 7-27 26 Table 7-19. FP-5 Objectives/Benefits Achievement Evaluation Data ...... 7-28 27 Table 7-20. FP-5 Impacts Evaluation Data ...... 7-29 28 Table 7-21. Settlement Alignment Levees, Relocations, and Land 29 Acquisition ...... 7-34 30 Table 7-22. Settlement Alignment Implementation/Technical Feasibility 31 Evaluation Data ...... 7-34 32 Table 7-23. Settlement Alignment Objectives/Benefits Achievement 33 Evaluation Data ...... 7-35 34 Table 7-24. Settlement Alignment Impacts Evaluation Data ...... 7-36 35 Table 7-25. Compact Alignment Levees, Relocations, and Land 36 Acquisition ...... 7-40 37 Table 7-26. Compact Alignment Implementation/Technical Feasibility 38 Evaluation Data ...... 7-41
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation v – October 2012 San Joaquin River Restoration Program
1 Table 7-27. Compact Alignment Objectives/Benefits Achievement 2 Evaluation Data ...... 7-42 3 Table 7-28. Compact Alignment Impacts Evaluation Data ...... 7-43 4 Table 7-29. Fresno Slough Dam Levees, Relocations, and Land 5 Acquisition ...... 7-47 6 Table 7-30. Fresno Slough Dam Implementation/Technical Feasibility 7 Evaluation Data ...... 7-47 8 Table 7-31. Fresno Slough Dam Objectives/Benefits Achievement 9 Evaluation Data ...... 7-48 10 Table 7-32. Fresno Slough Dam Impacts Evaluation Data ...... 7-49 11 Table 7-33. Bend 10 Options ...... 7-57 12 Table 7-34. Fresno Slough Dam Levees, Relocations, and Land 13 Acquisition ...... 7-60 14 Table 8-1. Initial Alternative Rankings for Fish Habitat and Passage 15 Criteria ...... 8-6 16 Table 8-2. Initial Alternative Rankings for Costs Criteria...... 8-7 17 Table 8-3. Initial Alternative Rankings for Implementation/Technical 18 Feasibility Perspective ...... 8-7 19 Table 8-4. Initial Alternative Rankings for Objectives/Benefits 20 Achievement Perspective...... 8-8 21 Table 8-5. Initial Alternative Rankings for Impacts Perspective...... 8-9 22 Table 8-6. Overall Initial Alternative Rankings ...... 8-10 23
24 Figures
25 Figure 1-1. Alternatives Formulation Process Diagram ...... 1-2 26 Figure 2-1 Aerial view of Reach 2B showing OHV tracks ...... 2-11 27 Figure 3-1 Restoration Flow hydrographs by restoration year type (Friant 28 releases) ...... 3-2 29 Figure 3-2 Restoration Flow hydrographs by restoration year type (Reach 30 2B) ...... 3-3 31 Figure 7-1. Levee Alignments for Floodplain Initial Alternatives ...... 7-2 32 Figure 7-2. Typical distribution of vegetation alliances along a Reach 2B 33 riparian bank section ...... 7-4 34 Figure 7-3. Plan View of Settlement Alignment ...... 7-32 35 Figure 7-4. Plan View of Compact Alignment ...... 7-38 36 Figure 7-5. Plan View of Fresno Slough Dam...... 7-45 37 Figure 7-6. Bend 10 Levee Alignment ...... 7-57 38 Figure 8-1 Summary of Evaluation Results ...... 8-1 39
Mendota Pool Bypass and Reach 2B Improvements Project vi – October 2012 Attachment A – Initial Alternatives Evaluation Table of Contents
1 Attachments
2 Attachment B ...... Evaluation Matrix 3
4
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation vii – October 2012 San Joaquin River Restoration Program
1 List of Abbreviations and Acronyms 2 2D two-dimensional 3 Act San Joaquin River Restoration Settlement Act 4 CCC Columbia Canal Company 5 CCID Central California Irrigation District 6 CDFG California Department of Fish and Game 7 CEQ Council on Environmental Quality 8 CEQA California Environmental Quality Act 9 CESA California Endangered Species Act 10 cfs cubic feet per second 11 CVFED Central Valley Floodplain Evaluation and 12 Delineation 13 CVP Central Valley Project 14 Delta Sacramento-San Joaquin Delta 15 DOE California Department of Water Resources, 16 Division of Engineering 17 DWR California Department of Water Resources 18 EIS/R Environmental Impact Statement/Environmental 19 Impact Report 20 ESA Endangered Species Act 21 FAF floodplain activation flow 22 FMWG SJRRP Fisheries Management Work Group 23 Flood Control Project Lower San Joaquin River Flood Control Project 24 Flood Operation Manual Flood Control Project’s Operation and 25 Maintenance Manual for Levee, Irrigation and 26 Drainage Structures, Channels and 27 Miscellaneous Facilities 28 fps feet per second 29 ft2 square feet 30 FSRAF floodplain salmonid rearing activation flow 31 Levee District Lower San Joaquin Levee District 32 NAVD88 North American Vertical Datum 1988 33 NEPA National Environmental Policy Act 34 NGVD29 National Geodetic Vertical Datum 1929 35 NMFS National Marine Fisheries Service 36 NRDC Natural Resources Defense Council
Mendota Pool Bypass and Reach 2B Improvements Project viii – October 2012 Attachment A – Initial Alternatives Evaluation Table of Contents
1 OHV off-highway vehicle 2 OHWM ordinary high water mark 3 O&M operations and maintenance 4 PEIS/R Program Environmental Impact Statement/ 5 Environmental Impact Report 6 Pool Mendota Pool 7 Project Mendota Pool Bypass and Reach 2B 8 Improvements Project 9 Reclamation U.S. Department of the Interior, Bureau of 10 Reclamation 11 Restoration Area the San Joaquin River Restoration area from 12 Friant Dam to the Merced River confluence 13 RM river mile 14 Secretary Secretary of the U.S. Department of the Interior 15 Settlement Stipulation of Settlement 16 SJRRP San Joaquin River Restoration Program 17 SSJVIC South San Joaquin Valley Information Center 18 State State of California 19 SWP State Water Project 20 TM Technical Memorandum 21 USACE U.S. Army Corps of Engineers 22 USC United States Code 23 USEPA U.S. Environmental Protection Agency 24 USFWS U.S. Fish and Wildlife Service 25 USGS U.S. Geological Survey
26
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation ix – October 2012 San Joaquin River Restoration Program
1 Definitions 2 For the purposes of the discussion in this technical memorandum, the following terms are 3 defined.
4 The Project – The Project refers to the portion of Reach 2B that will convey Restoration 5 Flows, the Mendota Pool Bypass, and all facilities related to implementation.
6 Reach 2B – Reach 2B refers either to the existing San Joaquin River between the 7 Chowchilla Bifurcation Structure and the Mendota Dam or to the future portion of that 8 reach which will contain Restoration Flows. Reach 2B does not include the Mendota 9 Pool Bypass.
10 Mendota Pool Bypass – Refers to the portion of the Project (channels, structures, and 11 other facilities) that will enable conveyance of Restoration Flows around the Mendota 12 Pool.
13 Pre-appraisal level themes – Pre-appraisal level themes are concepts used in an iterative 14 process of modeling coupled with public outreach and concept refinement. Themes were 15 refined and presented as initial options in the Initial Options Technical Memorandum 16 (TM) (SJRRP 2010e).
17 Initial Options – Initial options represent building blocks for future development of 18 project alternatives. Initial options were prepared for each project component and 19 presented in the Initial Options TM as a “menu” of preliminary ideas to meet the project 20 goals for each component. The initial options were further refined into Initial Alternatives 21 by subsequent data collection, analysis and analytical tools.
22 Initial Alternatives – Initial Alternatives are refined versions of the initial options and 23 were used to conduct the alternatives evaluation presented here. The evaluation assesses 24 the effects of the Initial Alternatives in several key resource areas (costs, schedule, fish 25 habitat and passage, habitat restoration, geomorphology, economics, socioeconomics, 26 land use, and threatened and endangered plants and wildlife). Initial Alternatives present 27 a range of alternatives for each major component of the Project, both the Reach 2B 28 improvements and the Mendota Pool Bypass.
29 Final Alternatives – The Final Alternatives are those Floodplain Initial Alternatives and 30 Bypass Initial Alternatives that were selected following the alternatives evaluation and 31 paired to form a whole (complete) project alternative. They are presented in the Project 32 Description TM, which will feed into the Environmental Impact 33 Statement/Environmental Impact Report (EIS/R). Final Alternatives are of a sufficient 34 detail to evaluate benefits and impacts, including project costs, land acquisition, and 35 mitigation needs. Each Final Alternative for the Project includes actions for both the 36 Mendota Pool Bypass and the Reach 2B improvements.
37 Mendota Pool Bypass and Reach 2B Improvements Project x – October 2012 Attachment A – Initial Alternatives Evaluation Table of Contents
1 This Draft Technical Memorandum (TM) was prepared by the San Joaquin River 2 Restoration Program (SJRRP) Team as a draft document in support of preparing an 3 Environmental Impact Statement/Environmental Impact Report (EIS/R) for the Mendota 4 Pool Bypass and Reach 2B Improvements Project (Project). The purpose for circulating 5 this document at this time is to facilitate early coordination regarding initial approaches 6 currently under consideration by the SJRRP Team with the Settling Parties, Third 7 Parties, other stakeholders, and interested members of the public. Therefore, the content 8 of this document may not necessarily be included in the Project EIS/R. While the SJRRP 9 Team is not requesting formal comments on this document, comments received will be 10 considered to the extent possible.
11
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Mendota Pool Bypass and Reach 2B Improvements Project xii – October 2012 Attachment A – Initial Alternatives Evaluation
1.0 Introduction This Project Description Technical Memorandum (TM) Attachment A documents the process for formulating and evaluating a broad range of Initial Alternatives to arrive at a reasonable range of complete alternatives. The alternatives will be evaluated further in the Project EIS/R for the Mendota Pool Bypass and Reach 2B Improvements Project (Project), a component of Phase 1 of the overall San Joaquin River Restoration Program (SJRRP). The SJRRP was established in late 2006 to implement the Stipulation of Settlement (Settlement) in Natural Resources Defense Council (NRDC), et al,. v. Kirk Rodgers, et al.
The U.S. Department of the Interior, Bureau of Reclamation (Reclamation), as the Federal lead agency under the National Environmental Policy Act (NEPA), and the California Department of Water Resources (DWR), as the State lead agency under the California Environmental Quality Act (CEQA), prepared this TM as an initial step in preparation of an Environmental Impact Statement/ Environmental Impact Report (EIS/R) for the Project. Federal authorization for implementing the Settlement is provided in the San Joaquin River Restoration Settlement Act (Act) (Public Law 111-11).
1.1 Purpose of this Attachment
This Attachment is intended to:
• Document the alternatives formulation and evaluation process for the Project consistent with NEPA and CEQA requirements • Describe Project goals and objectives and opportunities and constraints • Examine a reasonable range of alternatives to identify those that could meet the Settlement goals for the Project • Obtain input and feedback from the Implementing Agencies, Technical Work Groups, landowners, and other stakeholders involved in the Project
1.2 Summary of the Alternatives Formulation Process
As part of implementation of the Settlement, Reclamation and DWR began the NEPA/CEQA process on the site-specific projects, including the Mendota Pool Bypass and Reach 2B Improvements Project, by initiating preparation of an EIS/R. An early step in developing the EIS/R is the formulation of the project alternatives that would be addressed by the document. The process diagram shown in Figure 1-1 depicts the steps in the formulation process.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 1-1 – October 2012 San Joaquin River Restoration Program
Settlement Initial Options TM Improvements Refine Options Project Goals Initial Paragraphs into Initial and Objectives Options 11(a)(1) and Alternatives 11(a)(2)
Settlement Analytical Tools TM Restoration Goal Analyze and Water Evaluation Analytical Initial Management Criteria Tools Alternatives Goal with Tools
Evaluate Initial Alternatives with Criteria
Project Description TM
Project Final Description Alternatives
Figure 1-1. Alternatives Formulation Process Diagram
The initial guidance for developing the Project comes from language in the Settlement, specifically the Settlement’s goals and the Settlement defined improvements. The Settlement goals are:
The Restoration Goal (Settlement Paragraph 2):
… a goal of this Settlement is to restore and maintain fish populations in “good condition” in the main stem of the San Joaquin River below Friant Dam to the confluence of the Merced River, including naturally-reproducing and self-sustaining populations of salmon and other fish (the “Restoration Goal”).
The Water Management Goal (Settlement Paragraph 2):
…a goal of this Settlement is to reduce or avoid adverse water supply impacts to all of the Friant Division long-term contractors that may result from the Interim Flows and Restoration Flows provided for in this Settlement (the “Water Management Goal”).
The Mendota Pool Bypass and Reach 2B improvements defined in the Settlement are (Settlement Paragraph 11(a)):
Mendota Pool Bypass and Reach 2B Improvements Project 1-2 – October 2012 Attachment A – Initial Alternatives Evaluation 1.0 Introduction
(1) Creation of a bypass channel around Mendota Pool to ensure conveyance of at least 4,500 cfs from Reach 2B downstream to Reach 3. This improvement requires construction of a structure capable of directing flow down the bypass and allowing the Secretary to make deliveries of San Joaquin River water into Mendota Pool when necessary;
(2) Modifications in channel capacity (incorporating new floodplain and related riparian habitat) to ensure conveyance of at least 4,500 cfs in Reach 2B between the Chowchilla Bifurcation Structure and the new Mendota Pool bypass channel.
Alternatives formulation builds on the Settlement goals and project-specific improvements and progresses through three stages: initial options, Initial Alternatives, and Final Alternatives. Initial options represent the preliminary concepts and the basic components for project implementation. They were developed based on existing information and data, studies undertaken for the PEIS/R process, pre-appraisal level analyses and screening, as well as input from Program Work Groups, stakeholders, and the public. The initial options are described in the Initial Options TM (SJRRP 2010e). Subsequently, the initial options were refined into Initial Alternatives based on additional concept refinement and engineering analyses, preliminary cost-benefit analyses, additional data collection, and input from the Program, Program Work Groups, stakeholders, and the public. The Initial Alternatives represent a range of feasible implementation strategies incorporating appraisal-level design and analysis. The Initial Alternatives were evaluated based on the evaluation criteria and with the tools described in the Analytical Tools TM (SJRRP 2010f). This attachment documents the methods and results of the evaluation and makes recommendations for Final Alternatives to include in the main body of the Project Description TM.
1.3 Initial Alternatives Evaluation Process and Methods
The following steps outline the evaluation process. At this time only steps 1 through 4 were implemented. Step 5 was not conducted because it was found to not be necessary in order to arrive at a reasonable range of alternatives.
Step 1: Refine Evaluation Criteria • Identify criteria with meaningful, quantifiable results given stage of design and available field data • Identify criteria that are applicable to all alternatives, thereby providing a means of comparing alternatives • Group criteria into relevant factors, then group factors into relevant categories, then finally group categories into relevant perspectives so that alternatives can be compared at these different aggregated levels
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 1-3 – October 2012 San Joaquin River Restoration Program
Step 2: Develop Project Data • Using current level of design, field data, and appropriate assumptions, determine raw data for each criterion for each alternative
Step 3: Normalize Scores • Score each criterion on a range of 0 to 10, with 10 awarded to the alternative with the most desirable outcome. A score is normalized relative to the range of data values among the alternatives. • For criteria where high values of raw data indicate positive outcomes (i.e., benefits), the larger raw data values produce higher normalized scores, and smaller raw data values produce lower normalized scores. • For criteria where high values of raw data indicate negative outcomes (i.e., costs, impacts), the larger raw data values produce lower normalized scores, and smaller raw data values produce higher normalized scores. • Normalized scores are displayed on a qualitative scale of low, medium, and high.
Step 4: Alternatives Comparison (without weighting) • Calculate the average score to obtain the overall score for the subsequent aggregated levels (i.e., the factor level score is the average of the criteria scores under that factor; the category level score is the average of the factor scores under that category; the perspective level score is the average of the category scores under that perspective). • Aggregated scores are displayed on a qualitative scale of low, medium, and high.
Step 5: Alternatives Comparison (with weighting) • Using professional judgment, determine weights (i.e., fractions of 1, summing to 1 within a given level) for each criterion, factor, category, and perspective such that more important or influential items are assigned higher weights • Calculate the weighted average score to obtain the overall score for the subsequent aggregated levels (i.e., weighted average of criteria scores is the overall factor score; weighted average of factor is category; weighted average of category is perspective)
1.4 Organization of this Attachment
The content and format of this attachment are intended to dovetail with the future Project EIS/R. The attachment is organized as shown below.
Section 1.0 Introduction – summarizes the alternatives formulation process and describes the Project purpose and Settlement goals/improvements and the organization of this attachment.
Section 2.0 Opportunities and Constraints – provides an analysis of opportunities that exist outside the Project purpose and constraints within the study area.
Mendota Pool Bypass and Reach 2B Improvements Project 1-4 – October 2012 Attachment A – Initial Alternatives Evaluation 1.0 Introduction
Section 3.0 Goals and Objectives – presents the Project goals and objectives organized according to the overarching project purposes.
Section 4.0 Pre-Initial Options Analysis – describes decision making involved in the development of the initial options.
Section 5.0 Initial Options Refinement – describes the decision making and analysis involved in refining the initial options into Initial Alternatives.
Section 6.0 Initial Alternatives Evaluation Criteria – describes the criteria used in the alternatives evaluation.
Section 7.0 Initial Alternatives Descriptions – describes the Initial Alternatives for each component of the Project.
Section 8.0 Initial Alternatives Evaluation Results – describes the results of the evaluation, compares the Initial Alternatives based on the results, and recommends Final Alternatives as the reasonable range of alternatives to be evaluated in the Project EIS/R.
Section 9.0 Acknowledgments – provides a list of those who contributed to the document.
Section 10.0 References – provides a bibliography of sources cited throughout this attachment.
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Mendota Pool Bypass and Reach 2B Improvements Project 1-6 – October 2012 Attachment A – Initial Alternatives Evaluation
1 2.0 Opportunities and Constraints 2 Implementation of the Project may provide opportunities for improvements beyond the 3 scope of the project purpose. These opportunities may be incorporated or accommodated 4 in the Project incidentally or as a part of project alternatives. While incorporation of the 5 opportunities into the Project is not required, some opportunities may provide broad-scale 6 benefits to the terrestrial and aquatic ecosystem of the San Joaquin River or to the CVP 7 and SWP water supplies and flood management and may be considered for inclusion to 8 the extent that they do not negatively affect the ability of the Project to meet the Project 9 purpose, goals, and objectives.
10 In addition, some constraints on the planning process would limit the ability to implement 11 certain Project options and future alternatives. In general, constraints limit the range or 12 extent of options being considered, and in some cases, limitations set by constraints may 13 be used as a basis for development of evaluation criteria to be used during alternatives 14 formulation to examine the extent to which certain options meet Project goals and 15 objectives.
16 2.1 Opportunities
17 2.1.1 Habitat Improvement for Other Native and Special Status Species 18 The restoration of the San Joaquin River for the purposes of reintroduction of Chinook 19 salmon to reaches between the Merced River and Friant Dam may incorporate restoration 20 of native floodplain and in-channel habitats. Restoration of these habitats is one of the 21 Project purposes and is likely to benefit other native and potentially special status 22 terrestrial and aquatic species such as Swainson’s hawk (Buteo swainsoni), greater 23 sandhill crane (Grus canadensis tabida), etc. Benefits to other native species would be 24 realized through the re-introduction of perennial base flows as well as seasonal high 25 flows in the River, which in turn would promote the establishment of indigenous riparian 26 vegetation. Well-established native plant communities in the floodplain would support 27 rich and diverse native flora, including potentially, special status plant species, would 28 effectively prevent invasive vegetation encroachment, and would provide foraging habitat 29 and shelter for native wildlife species.
30 Specific opportunities include the following:
31 • Restoring river-floodplain connectivity and longitudinal connectivity of riparian 32 vegetation near the channel (without major breaks in the distribution of woody 33 vegetation except where natural conditions prevent establishment of native trees 34 or shrubs) that can provide cover and habitat for a variety of wildlife species 35 • Creating or maintaining a combination of diverse habitats required by selected 36 wildlife species, such as species that depend on concurrence of aquatic, wetland
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 2-1 – October 2012 San Joaquin River Restoration Program
1 or riparian, and upland habitats to meet various life stage requirements (e.g., 2 western pond turtle, Swainson’s hawk) 3 • Enhancing landscape connectivity between the river corridor and adjacent areas of 4 ecological significance (e.g., wildlife refuges and other protected lands, 5 biodiversity “hotspots,” adjacent sloughs or tributary channels with existing 6 riparian habitat, wildlife movement corridors, and private natural preserves such 7 as the Mendota Wildlife Area) 8 • Protecting, restoring, or enhancing special status vegetation alliances and plant 9 species
10 2.1.2 Open Space & Mitigation 11 Opportunities for open space and wetlands/waters and habitat/species mitigation for 12 Project-related impacts are available in the areas south of the proposed Mendota Pool 13 Bypass. It is expected that agricultural land between the Mendota Pool Bypass 14 configuration and the existing river would not support production in the future condition 15 due to lack of drainage. These lands may be acquired as part of the project due to the 16 impacts to agricultural utility, and therefore, may be available for open space 17 conservation and mitigation. Some of these lands have been fallowed in anticipation of 18 the acquisition.
19 Open space and mitigation may also be available in the two river bends (west and east 20 loops) near the upstream end of the Project. These areas are occasionally used for cattle 21 grazing but are substantially non-native grasslands. Potential exists for habitat 22 improvements to be incorporated in these areas that may provide some mitigation credit 23 for the Project.
24 The property along the south bank at the upstream end of the Project currently exhibits 25 natural topography, is connected to the river corridor, and management of this land is 26 virtually unchanged since pre-Friant Dam times. It is believed that high quality, native 27 species habitat is extensive on this property, which appears to extend in similar fashion 28 south to Alkali Sink Ecological Reserve. Significant mitigation and conservation 29 opportunities are available on this parcel, and the potential to include this parcel with the 30 Project could be explored further.
31 Finally, opportunities for open space and mitigation may be available on portions of 32 parcels that may be acquired for the Project but are outside of the area required to build 33 the Project. For example, a whole parcel may be purchased for the Project even though 34 the full extents are not required to build the project. This may occur when the property 35 which remains outside the Project extents has limited use or value for agricultural 36 production.
37 2.1.3 Recreation 38 Existing water-related recreational opportunities on the Reach 2B segment of the San 39 Joaquin River are limited because the upper half of the River reach was dry most years 40 prior to Interim Flows, and even the downstream inundation associated with the Pool
Mendota Pool Bypass and Reach 2B Improvements Project 2-2 – October 2012 Attachment A – Initial Alternatives Evaluation 2.0 Opportunities and Constraints
1 water is drained bi-annually for several weeks. Moreover, areas immediately adjacent to 2 the riverbed are privately owned, and public access is limited.
3 Currently, the nearest vehicular access to the riverbed is San Mateo Avenue. The 4 primary nearby water-related recreational opportunities are outside the immediate Reach 5 2B channel area at Mendota Pool, approximately four miles from the San Mateo Avenue 6 crossing, which offers angling.
7 Future recreational activities along Reach 2B would be similarly limited if the Project 8 were not implemented. While population in the Project area and vicinity would likely 9 increase at rates common for the west side of the San Joaquin Valley, any increased 10 recreational demands would be directed to nearby recreational venues, including 11 Mendota Pool and San Luis Reservoir (approximately 40 miles to the northwest).
12 Implementation of the Reach 2B Project may offer some expansion in recreational 13 opportunities. However, it would be necessary to consider these opportunities relative to 14 the Restoration Goal (Settlement Paragraph 2):
15 … a goal of this Settlement is to restore and maintain fish populations 16 in “good condition” in the main stem of the San Joaquin River below 17 Friant Dam to the confluence of the Merced River, including 18 naturally-reproducing and self-sustaining populations of salmon and 19 other fish (the “Restoration Goal”).
20 Habitat restoration goals for Reach 2B may be found in Section 3.4 of this document. 21 Consequently, if implementation of the Project would provide greater public access to 22 Reach 2B, it is expected that appropriate restrictions on fishing and other activities in and 23 near the water that could endanger salmon or result in trespassing on private lands would 24 be implemented.
25 2.1.4 Water Quality 26 Implementation of the Project has the potential to improve water quality to the extent that 27 native aquatic, riparian, and floodplain vegetation may remove and uptake some 28 pollutants dissolved in San Joaquin River flows. Greater water quality improvements may 29 be realized through nutrient cycling and pollutant uptake following sediment deposition 30 during high flow events where floodplains are inundated. However, because Millerton 31 Lake has good water quality and there are minimal agricultural return flows upstream of 32 Reach 2B, water quality is expected to be good in the Reach 2B and, therefore, will not 33 likely need improvement.
34 2.1.5 Education 35 If implementation of the Project would provide greater public access to Reach 2B, the 36 Project could also incorporate opportunities for education for students, land owners, 37 restoration specialists, recreational enthusiasts, and the general public. River processes, 38 native wildlife and habitats, water management, and ecological restoration are all topics 39 that could be incorporated into education campaigns involving interpretive signage, trails, 40 and field trips as appropriate.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 2-3 – October 2012 San Joaquin River Restoration Program
1 2.1.6 Flood System 2 The Lower San Joaquin River Flood Control Project (Flood Control Project), authorized 3 by Congress in 1944 to protect irrigated agricultural lands and associated developments, 4 is operated and maintained by the Lower San Joaquin Levee District (Levee District) 5 under the Flood Control Project’s Operation and Maintenance Manual for Levee, 6 Irrigation and Drainage Structures, Channels and Miscellaneous Facilities (Flood 7 Operation Manual). The Project offers some opportunity for improving the flood system 8 and flood operations within the San Joaquin River Reach 2B. The current channel 9 capacity of 2,500 cfs would be increased to at least 4,500 cfs. Although not analyzed as 10 part of this TM, the increased conveyance may provide opportunities for improving flood 11 operations during certain flood scenarios. The ability to accommodate higher flows 12 during flood releases is dependent on the downstream capacity of the system. Currently, 13 the Project will not alter the Flood Operations Manual.
14 2.2 Constraints
15 2.2.1 Settlement and Act Requirements 16 The Settlement requirements and conditions of the Act place legal constraints on the 17 Project. Specifically, Settlement Paragraphs 11(a)(1) and 11(a)(2) require:
18 [Paragraph 11(a)] (1) Creation of a bypass channel around Mendota 19 Pool to ensure conveyance of at least 4,500 cfs from Reach 2B 20 downstream to Reach 3. This improvement requires construction of a 21 structure capable of directing flow down the bypass and allowing the 22 Secretary to make deliveries of San Joaquin River water into Mendota 23 Pool when necessary;
24 [Paragraph 11(a)] (2) Modifications in channel capacity 25 (incorporating new floodplain and related riparian habitat) to ensure 26 conveyance of at least 4,500 cfs in Reach 2B between the Chowchilla 27 Bifurcation Structure and the new Mendota Pool bypass channel.
28 2.2.2 Other Legal and Regulatory Compliance 29 The Project must comply with various Federal, State, and local laws, regulations, 30 executive orders, and policies. The alternatives developed for the Project must 31 demonstrate compliance with applicable regulatory requirements as part of the 32 NEPA/CEQA process. Additionally, regulatory compliance is needed to obtain the many 33 permits and approvals that would be required prior to project construction. Many of the 34 laws and regulations, such as the Clean Air Act and the Clean Water Act, set thresholds 35 or standards for certain types of impacts associated with a project. Consideration of these 36 thresholds early in the alternatives formulation process is important in order to avoid 37 adverse environmental effects, project delays, and costly mitigation. Table 2-1 presents a 38 brief list of applicable laws, regulations, executive orders, and policies that the Project 39 must comply with. These regulatory requirements would be considered throughout the 40 alternatives formulation process and would be updated as the options are further refined.
Mendota Pool Bypass and Reach 2B Improvements Project 2-4 – October 2012 Attachment A – Initial Alternatives Evaluation 2.0 Opportunities and Constraints
1 Table 2-1 2 Laws, Regulations, Executive Orders, and Policies Federal State Bald and Golden Eagle Protection Act California Clean Air Act Clean Air Act California Code of Regulations Title 23: Central Clean Water Act, Sections 401, 402, 404 Valley Flood Protection Board Endangered Species Act, Section 7 California Endangered Species Act Executive Order 11988, Flood Hazard Policy California Environmental Quality Act Executive Order 11990, Protection of Wetlands California Fish and Game Code, Section 1602 Executive Order 12898, Environmental Justice California Land Conservation Act (Williamson Policy Act) Executive Order 13007, Indian Sacred Sites California Native American Graves Protection Executive Order 13112, Invasive Species and Repatriation Act Executive Order 13186, Migratory Birds California Native Plant Protection Act Farmland Protection Policy Act California Native Plant Society Species Fish and Wildlife Coordination Act Designations Indian Trust Assets (U.S. Department of the California Office of Historic Preservation Interior Departmental Manual Part 512) California Register of Historic Resources National Environmental Policy Act California Water Rights National Historic Preservation Act, Section 106 Environmental Justice Public Resources Code Native American Graves Protection and 65040.12(e) Repatriation Act Porter-Cologne Water Quality Control Act Magnuson-Stevens Fishery Conservation and Public Resources Code 6501-6509 Lease of Management Act Public Lands under State Lands Commission Migratory Bird Treaty Act Surface Mining and Reclamation Act Rivers and Harbors Act, Section 9, (33 USC Local 401), Section 10 (33 USC 403) and 14 (33 USC 408) Fresno County Code 13.08 Private Improvements within Road Rights-of-Way Madera County Code Section 14.50 Grading Permit and Section 17.32 Road Encroachment Permit San Joaquin Valley Air Pollution Control District Rule 2010 – Authority to Construct/Permit to Operate 3
4 2.2.3 Operations for Flood Releases and Water Deliveries 5 The Project will consider three different conditions under which releases are or would be 6 made from Friant Dam: Restoration Flows, flood releases, and water deliveries. While 7 the Project is primarily focused on building the reach for conveyance of the Restoration 8 Flows, the factors and conditions surrounding the management of flood releases and 9 water deliveries to Mendota Pool are constraints on the available Project options, 10 particularly for structures. The PEIS/R includes information on the Program approach to 11 flood operations and water deliveries (SJRRP 2011a).
12 The Exchange Contract (Reclamation 1967) defines that a maximum of 2,316 cfs may be 13 required to be delivered to the Pool from Friant via Reach 2B, and also defines to varying 14 extents maximum monthly flow magnitudes and volumes that may be requested for 15 delivery. To date, water deliveries to the Pool have never been made via releases from 16 Friant and the San Joaquin River; in addition, current planning models do not anticipate 17 any future occurrence of a Friant delivery. Due to the lack of precedent and predictive 18 cases, the timing of these delivery requests and the delivery duration are unknown, and it
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 2-5 – October 2012 San Joaquin River Restoration Program
1 is also unknown what coincident flow may be available to meet Restoration Flows. 2 Therefore, the alternatives for the Mendota Pool Bypass Bifurcation Structure would 3 need to incorporate the flexibility to divert a range of flows to the Mendota Pool Bypass, 4 the Pool, or both. The structure may also need to incorporate fish screens that would 5 function under a variety of flow ranges and splits to screen fish from the Pool.
6 Flood operations are managed from a risk perspective for the purposes of protecting 7 public health and safety and property. The specific flood operations in Reach 2B are 8 dependent on flow entering the Pool from Fresno Slough, as well as the flow at the 9 Chowchilla Bifurcation Structure. The O&M manual recommends flood operations based 10 on flow rates in Reach 2B for varying flow magnitudes in Fresno Slough and the 11 Chowchilla Bifurcation Structure (Reclamation Board 1969). The levee districts have the 12 latitude to operate facilities in the manner that will best protect public health and safety 13 and property. Since the project specific EIS/Rs establish the improvements that would 14 safely convey the Restoration Flows in the various reaches, it is assumed that conveyance 15 of Restoration Flows coincident with flood flows are not in conflict, and the system can 16 be managed in a manner that will protect public health and safety and property while also 17 maintaining the flexibility to provide some level of flow in the principal migration 18 pathways (i.e., Mendota Pool Bypass). However, future agreements and/or changes in the 19 Flood Operation Manual would be necessary to provide for this type of management. 20 These agreements and/or possible changes to the Flood Operation Manual are outside of 21 the scope of this Project and would likely undergo separate review and approval, if 22 executed. For the purposes of this evaluation it is understood that protection of public 23 health and safety and property takes precedence and certain conditions may arise where 24 ensuring ideal flows and pathways for fish migration may not be obtainable.
25 As part of development of the Initial Alternatives, the following order of priorities for 26 flow management was considered.
27 • 1st Priority: Flood operations for the protection of public health and safety and 28 property. 29 • 2nd Priority: Water deliveries to the Exchange Contractors. 30 • 3rd Priority: Restoration Flows. 31 • 4th Priority: Flood releases to meet water supply delivery contracts. 32 Under this management prioritization, several specific scenarios may occur, but in 33 general, it is assumed that:
34 • Flood releases from Friant may be routed through the Mendota Pool Bypass 35 pending other flood operations considerations (e.g., Fresno Slough contributions) 36 or they may be routed through both the Mendota Pool Bypass and the Pool 37 • Water deliveries may reduce Restoration Flows in the Mendota Pool Bypass to a 38 maximum of 2,000 cfs, given the 4,500 cfs total reach capacity and the 2,500 cfs 39 delivery, but otherwise do not restrict Restoration Flows in the reach
Mendota Pool Bypass and Reach 2B Improvements Project 2-6 – October 2012 Attachment A – Initial Alternatives Evaluation 2.0 Opportunities and Constraints
1 2.2.4 Fish Passage 2 The following is a summary of operational and site constraints that may limit the ability 3 of the Project to meet the project goals and objectives pertaining to fish passage in the 4 channel and at structures under Restoration and flood flows:
5 1. Flow routing, particularly during flood and Pool delivery scenarios will affect the 6 range and types of options presented. Since the reach will be conveying flow for three 7 purposes (floods, water deliveries, and fish), the various structure operational 8 scenarios need to be understood such that new structures and modifications of 9 existing structures can be configured to provide adequate conditions for fish over the 10 widest range of potential flow routing scenarios. Channel and habitat connectivity 11 should be considered during flood flows analysis in order to support meeting fishery 12 restoration objectives.
13 2. Low flow conditions (100-350 cfs releases at Friant Dam) may preclude passage up 14 or downstream for native fish in the channel due to upsteam uses, losses to 15 groundwater, and the limited depth of flow in the wide and sandy channel of Reach 16 2B. These flows can occur in any water year type in the summer following spring 17 pulse flows and in the winter following fall pulse flows, so they may only have 18 limited effect on fish passage. Reach 2B prior to Interim Flows had very poor aquatic 19 habitat to support fish. The channel is wide, with little morphological development. 20 Substrate is homogenous and aquatic habitat features are limited to minor bars and 21 shallow depressions. The rate of development of riparian vegetation may be a key in 22 improving channel conditions. Encouraging the establishment of a low flow channel 23 in a sand bed without benefit of riparian vegetation may be a challenge. Recreational 24 activities in Reach 2B upstream of San Mateo Avenue crossing may preclude re- 25 establishment of riparian vegetation and a functional channel and floodplain (see 26 Section 2.2.11).
27 3. The number of existing and proposed structures in Reach 2B could become a factor in 28 the success of migrating native fish completing their life cycle. While potential 29 structures will be designed to meet NMFS and DFG criteria for passage, and existing 30 structures may be modified to meet these criteria, the structures will not be a natural 31 system. The channel, floodplain, and structures need to be designed to allow river 32 connectivity and passage flows to be sustained over the structures for a sufficient 33 period of time to provide for fish to pass over all the structures on their upstream 34 movements into Reach 2A and for downstream passage of juveniles into Reach 3. 35 The structures also need to be designed to minimize the effects of predation and 36 localized hydraulic changes on fish.
37 4. Routing of flood flows should consider effects to the native fish populations with the 38 understanding that the foremost priority during flood operations will be for the 39 protection of public health and safety and property (see Section 2.2.3). Flood routing 40 decisions are not made by the SJRRP, but are carried out by other entities, including 41 the Central Valley Flood Protection Board and the Levee District.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 2-7 – October 2012 San Joaquin River Restoration Program
1 2.2.5 Special Status Species 2 There are known occurrences and the potential for occurrences of special status plant and 3 wildlife species native to the San Joaquin River corridor and specifically the area in and 4 adjacent to the Project. Impacts to species and their habitats are regulated through Federal 5 programs via the Endangered Species Act (ESA) and through State programs via the 6 California Endangered Species Act (CESA). By law, those responsible for the Project 7 must incorporate assessment, coordination, permitting, and avoidance, minimization, and 8 mitigation for impacts to special status species and their regulated habitats.
9 2.2.6 Cultural and Historical Resources 10 Project has the potential to affect cultural and historical resources within the Project area 11 due to proposed grading, construction of structures, land use change, and possible 12 increased extent and depth of flooding. An assessment of the presence of cultural and 13 historic resources would be addressed in a separate TM. Impacts to cultural and historical 14 resources within the area of potential effect of the Project must be avoided, minimized, or 15 mitigated, as applicable.
16 2.2.7 Land Use/Agriculture and Socioeconomic/Environmental Justice
17 Land Use/Agriculture 18 Implementation of the Project would have a direct affect on landowners and land uses 19 proximate to Reach 2B. The land proximate to Reach 2B is primarily in agricultural 20 production with permanent (high value) crops. The land is within the water service areas 21 of Columbia Canal Company, (one of the San Joaquin River Exchange Contractors), the 22 Aliso Water District, and the Farmers Water District. Much of the agricultural land is 23 planted in permanent crops, including almonds, pistachios, palms, and wine grapes (Houk 24 2009). Annual crops are primarily corn and silage (in support of the local dairy industry) 25 alfalfa, and melons. None of the affected land is typically used to grow vegetables.
26 Socioeconomic/Environmental Justice Issues 27 Environmental justice is defined as the potential for a project to disproportionately affect 28 disadvantaged populations including low income and minority populations. The potential 29 for the Reach 2B Project to affect these groups would be associated with economic 30 impacts, as few people live in the affected Project area. Because the riverbed, prior to 31 Interim Flows, was partially dry and public access is very limited, little potential exists 32 for the Project to affect subsistence fishing activity by disadvantaged populations.
33 Data from the 2000 Census of Population and Housing show that agriculture and 34 agriculture-related industries provide most of the household employment in the area.
35 Construction, implementation, and maintenance of the Reach 2B Project have the 36 potential to adversely affect agricultural land proximate to the River because of the land 37 acquisition that would be required to construct both levee setbacks for the purposes of 38 increasing channel capacity and creating habitat to support anadromous fisheries. The 39 number of acres affected would vary by alternative. The loss of agricultural production 40 land may adversely affect the socioeconomic and environmental justice characteristics of 41 the affected area. Any reduction in agricultural land use can be expected to affect not
Mendota Pool Bypass and Reach 2B Improvements Project 2-8 – October 2012 Attachment A – Initial Alternatives Evaluation 2.0 Opportunities and Constraints
1 only agricultural production itself, but also the many industries which support and are 2 supported by production agriculture. Construction-related activities and purchases of 3 goods and services in the project area would at least partially offset the reductions in 4 agricultural economic activity. The economic areas most likely to be affected include the 5 incorporated cities of Firebaugh and Mendota, both in Fresno County, and 6 unincorporated areas in both Fresno and Madera Counties.
7 2.2.8 Seepage 8 The Project design criteria will address any seepage effects on adjacent agricultural lands 9 due to the increased flow frequency, quantity, and duration in the River channel and 10 floodplain under the Restoration Flows. Seepage is a concern for levee stability and 11 because it can cause damage to agricultural crops through increased root zone 12 groundwater saturation and/or increased soil salinity which may decrease yield or cause 13 die-off of crops, thus affecting lands outside of the direct Project footprint. An analysis of 14 the potential for seepage and the monitoring and action thresholds for the Project area has 15 been developed in the Draft Seepage Management Plan (SJRRP, 2009c), and further 16 development of this plan is expected.
17 2.2.9 River Crossings 18 One river crossing exists in Reach 2B at San Mateo Avenue. This crossing is a low water 19 crossing with a Madera County public right-of-way to the centerline of the river on the 20 north side and no right-of-way south of the centerline in Fresno County (Fresno County 21 public right-of-way picks up approximately 3,600 feet south of the river). In addition, a 22 future crossing at Road 10 ½ is anticipated over the bypass channel (Settlement and 23 Compact Alignments). Historically, access across the river at San Mateo Avenue could 24 occur during most times because the channel flowed infrequently. With the introduction 25 of the Restoration Flows, access may become limited because the Restoration Flows 26 could overtop the roadway surface more frequently.
27 The need to maintain the San Mateo Avenue crossing, if needed and appropriate, provide 28 the Road 10 ½ crossing, and limit overtopping flows at both will constrain the type of 29 crossing design as well as affect the construction and maintenance costs. Coordination 30 with landowners and Counties was conducted to help determine access needs (times of 31 year, equipment types, etc.) and crossing frequency. The crossings also have the potential 32 to affect fish passage, sediment transport, and geomorphic processes.
33 2.2.10 Geomorphology 34 The geomorphic constraints for this project include channel base elevations, longitudinal 35 slope, and the imposed flow and sediment supply regimes. Channel base elevations at the 36 up and downstream ends of the Project are fixed because the Project must tie into channel 37 elevations of Reach 2A and 3. Actual slope of the channel is dependent on channel length 38 or sinuosity. In the case of the proposed Mendota Pool Bypass Settlement and Compact 39 alignment options, the length of the river channel would be shortened over the current 40 length. This in turn increases the slope of the bed profile between the two bypass tie-in 41 locations. Increases in slope effectively increase the sediment transport capacity of the 42 reach, which may result in erosion and degradation.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 2-9 – October 2012 San Joaquin River Restoration Program
1 To maintain long-term stability, the incoming sediment supply must be transported 2 through the Project reach maintaining sediment continuity. The incoming sediment load 3 is a boundary condition, and Project constraint, defined by the future flows and sediment 4 transport from the upstream reaches. To maintain stability during discrete events 5 (particularly at structures), the transient sediment regime during individual high and low 6 flow events must also be understood.
7 Rivers are dynamic systems that change over time and space due to imposed 8 environmental conditions. Meander migration is a natural process of a rivers lateral 9 movement across valley floors. It is a result of erosion on the outer bank of meander 10 bends and deposition on the inner bars forming floodplain surfaces. Migration is a 11 complex process not fully understood involving various types of movement. As a river 12 channel migrates, ideally, it maintains its general shape (width, depth and slope) or 13 “dynamic equilibrium”.
14 Meander migration may not be a desirable physical process to reestablish. However, 15 some form of erosion and deposition is expected in rivers and stream systems. The wider 16 the floodplain alternative, the more natural lateral migration processes in river alignment 17 may be accommodated. As the corridor width of the options decreases, the river channel 18 is constrained to its current location, and the need for engineered structures to restrict 19 migration increases.
20 2.2.11 Recreation 21 Prior to Interim Flows, recreational activities occurring on the site primarily consisted of 22 operating off-highway vehicles (OHVs) in areas upstream of the San Mateo Avenue 23 crossing. OHV use in the river corridor post-restoration is potentially a significant site 24 constraint during low flows. With the fine sand bed that exists in the river channel, 25 vegetation is the only means of stabilizing the low flow channel, and establishment of 26 vegetation would be greatly hindered by OHV use, which would continuously remove 27 emerging vegetation and prevent establishment of successional vegetation (see Figure 28 2-1). The prevention of the establishment of vegetation has strong implications for 29 geomorphic processes as well as for providing appropriate fish habitat. Prevention of 30 unauthorized vehicular access to the restoration area would be key to encouraging the 31 establishment of vegetation, wildlife habitats, and geomorphic stability.
Mendota Pool Bypass and Reach 2B Improvements Project 2-10 – October 2012 Attachment A – Initial Alternatives Evaluation 2.0 Opportunities and Constraints
1
2 Figure 2-1 3 Aerial view of Reach 2B showing OHV tracks
4 2.2.12 Illegal Dumping 5 Illegal dumping is occurring at the San Mateo Avenue crossing, which is the primary 6 public access point to the river in Reach 2B. Large areas on both the upstream and 7 downstream sides of this crossing are affected by the dumping of trash, furniture, 8 appliances, and other items. This material has the potential to not only affect the 9 operation and maintenance of existing and proposed structures (by clogging or fouling 10 San Mateo Avenue culverts, Mendota Pool Bypass Bifurcation Structure, etc.), but could 11 also have a large effect on water and habitat quality. Additionally, the costs associated 12 with characterizing, removing, and disposing of any contaminated material are potentially 13 significant. The effects on structures and water and habitat quality have repercussions for 14 the ability of the reach to support fish uses. The material should be removed and 15 measures to prevent additional dumping should be incorporated into the Project.
16 2.2.13 Sand Mining 17 Evidence of sand mining is apparent within Reach 2B between the Chowchilla 18 Bifurcation Structure and San Mateo Avenue. This results in the presence of deep, 19 unnatural pools in the river channel and large stockpiles of sand adjacent to the river 20 corridor. Sand mining may have adverse effects on riparian vegetation, native and special 21 status species, channel geomorphology, and seepage. It is recommended that these 22 operations be discontinued and that the Project include measures to prevent future mining 23 operations within the Project area. Sand mining does not refer to future sediment
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 2-11 – October 2012 San Joaquin River Restoration Program
1 management or maintenance dredging that may occur as part of the Project, which would 2 be conducted according to the Sediment Management Plan.
3
Mendota Pool Bypass and Reach 2B Improvements Project 2-12 – October 2012 Attachment A – Initial Alternatives Evaluation
1 3.0 Goals and Objectives 2 Project goals and objectives provide a comprehensive vision for meeting the project 3 purpose. Goals denote broad statements of intent that provide focus or vision for 4 planning. The project goals provide a basis upon which specific objectives are formed. 5 The objectives are intended to be well grounded, rooted in the project realities, and 6 measurable to the extent possible so the project would have a quantitative means of 7 evaluating project success. It should be noted that some biological objectives may not be 8 quantifiable. Goals and objectives are presented for the following categories: flow 9 conveyance, water supply, fish habitat and passage, habitat restoration, seepage, and 10 geomorphology.
11 Many of the goals and objectives are interrelated. For example, flow conveyance will be 12 necessary to support fish passage and habitat restoration. While goals and objectives are 13 organized by resource area, it should be understood that the Project should meet all the 14 goals and objectives.
15 The goals and objectives presented below were assembled from studies and documents 16 prepared specifically for the SJRRP as well as non-SJRRP scientific and guidance 17 documents representing the best available knowledge on the resource areas.
18 3.1 Flow Conveyance
19 Flow conveyance goals and objectives refer to the capacity of the channel, bypass, and 20 structures to accommodate the range of Restoration Flows and flood releases. Restoration 21 releases from Friant Dam are shown in Figure 3-1, and associated Restoration Flows 22 expected in Reach 2 are shown in Figure 3-2.
23 Flow Conveyance Goal 24 Improve flow conveyance within Reach 2B between the Chowchilla Bifurcation 25 Structure and the Mendota Pool Bypass to accommodate at least 4,500 cfs (Settlement 26 Paragraph 11(a)(2)), and provide at least 4,500 cfs of flow conveyance in the proposed 27 Mendota Pool Bypass (Settlement Paragraph 11(a)(1)).
28 Objectives 29 1. The entire Project channel/floodplain reach shall convey the full range of flows, up to 30 at least 4,500 cfs.
31 2. Construct a bypass channel around Mendota Pool to convey the full range of flows, 32 up to at least 4,500 cfs, to Reach 3.
33 3. The proposed San Mateo Avenue and Road 10 ½ crossings, if built, shall be designed 34 to convey the full range of flows, up to at least 4,500 cfs.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 3-1 – October 2012 San Joaquin River Restoration Program
1 4. The proposed Mendota Pool Bifurcation structure shall divert the full range of flows 2 (up to 4,500 cfs) into the Mendota Pool Bypass channel.
3 5. The proposed Mendota Pool Bifurcation Structure shall prevent, to the extent 4 practicable, water loss below the normal pool elevations to maintain the Pool 5 elevation under proposed conditions. The Pool currently operates at a water surface 6 elevation of about 152.7 feet (NGVD29) or 155.0 feet (NAVD88).
7
8
9 Source: SJRRP 2008 10 Figure 3-1 11 Restoration Flow hydrographs by restoration year type (Friant releases)
Mendota Pool Bypass and Reach 2B Improvements Project 3-2 – October 2012 Attachment A – Initial Alternatives Evaluation 3.0 Goals and Objectives
1
2 1 Hydrographs reflect assumptions about seepage losses and tributary inflows which are specified in the Settlement. 3 2 Reach 2B hydrographs are labeled as Reach 3 in Settlement Exhibit B. 4 Figure 3-2 5 Restoration Flow hydrographs by restoration year type (Reach 2B)
6 3.2 Water Supply
7 Water supply goals and objectives refer to provisions of the Project which will enable the 8 continued ability to deliver contract water from Friant Dam to Mendota Pool via the San 9 Joaquin River. Provisions for sufficient capacity outside the Project area and provisions 10 for securing the water required by the contract are beyond the purpose of this Project.
11 Water Supply Goal 12 Accommodate water deliveries and flood releases to Mendota Pool at the Mendota Pool 13 Bypass Bifurcation Structure (Settlement Paragraph 11(a)(1)).
14 Objectives 15 1. Under certain flood operation scenarios, it may be preferred to direct all or a portion 16 of flood releases (see Section 2.2.3 for a summary of flood operations constraints) 17 into the Pool. Should all flood flows be required in the Pool, the Mendota Pool 18 Bypass Bifurcation Structure may require the flexibility to prevent or limit flows into 19 the Mendota Pool Bypass.
20 2. The Mendota Pool Bypass Bifurcation Structure shall be capable of providing up to a 21 2,500 cfs delivery to the Pool when directed by the Secretary. During these delivery
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 3-3 – October 2012 San Joaquin River Restoration Program
1 flows, the structure shall have the flexibility to convey a range of flows (100-2,000 2 cfs) above the delivery flow through the Mendota Pool Bypass.
3 3.3 Fish Habitat and Passage
4 Restoration of aquatic habitat and fish passage for the purposes of establishing fish 5 populations involves several interrelated processes:
6 • Determining the correct habitat components to include in the system 7 • Understanding how those components would function with the hydrology and 8 geomorphology of the system 9 • Understanding how the flow routing and river conditions would interact to restore 10 the hydrologic connectivity 11 Fisheries goals for the Restoration of the San Joaquin River are derived from the 12 Restoration Goal in the Settlement (Settlement Paragraph 2):
13 … a goal of this Settlement is to restore and maintain fish populations 14 in “good condition” in the main stem of the San Joaquin River below 15 Friant Dam to the confluence of the Merced River, including 16 naturally-reproducing and self-sustaining populations of salmon and 17 other fish (the “Restoration Goal”).
18 Priority is given to spring-run Chinook salmon populations, while fall-run Chinook 19 populations are also included in the SJRRP fisheries goal (SJRRP 2010c). In this regard, 20 an important component of the SJRRP is to convey flows for fish passage and migration 21 from Reach 1 to Reach 5. Reach 1 contains all of the spawning and incubation habitat, 22 and nearly all of the year-round rearing habitat for spring-run Chinook salmon (SJRRP 23 2010c). Reaches 2 through 5 (as well as the remainder of the San Joaquin River from the 24 Merced River confluence to the Delta) would support fry to juvenile rearing during the 25 outmigration life stages for spring- and fall-run salmon. Rearing during the outmigration 26 life stage is described by the term “transient rearing.” A second component of the Project 27 is to provide suitable habitat and passage conditions for upstream migrating adults.
28 SJRRP fisheries goals and objectives are presented in Chapter 3 of the Fisheries 29 Management Plan (SJRRP 2010c). Fishery restoration and management goals are applied 30 throughout the Restoration Area – i.e., the San Joaquin River from confluence with the 31 Merced River to Friant Dam. Individual reaches have different goals since the reaches are 32 not all similar in habitat function and have somewhat different issues regarding flow 33 conveyance and fish passage. Therefore not all restoration and management goals are 34 applicable to all reaches.
35 The Fisheries Management Plan divides goals into Population Goals and Habitat Goals. 36 Goal statements are general statements identifying the elements necessary to restore the 37 fish populations and habitat in the entire San Joaquin River Restoration Project Area. 38 Each Population or Habitat Goal in the Fisheries Management Plan is supported by a
Mendota Pool Bypass and Reach 2B Improvements Project 3-4 – October 2012 Attachment A – Initial Alternatives Evaluation 3.0 Goals and Objectives
1 series of more detailed Objectives that in some cases provide a target restoration 2 condition for the fish population or the habitat condition once the project is implemented 3 and operating.
4 3.3.1 Fish Habitat Goals and Objectives 5 The following fish habitat goals and objectives apply to Reach 2B. The goals correspond 6 to those found in the Fisheries Management Plan for the Restoration Area and for 7 individual reaches (Table 3-1).
8 Fish Habitat Goal 1 9 Provide functional rearing habitat for juvenile salmon for the purposes of transient 10 rearing during outmigration.
11 Objectives 12 1. Create habitat conditions (suitable depth, velocity, and temperature) for juvenile 13 foraging during winter and spring.
14 2. Minimize fish and bird predation at structures.
15 3. Create habitat conditions (suitable depth, velocity, and temperature) that support 16 successful outmigration.
17 4. Include seasonally inundated floodplain with suitable habitat conditions for juvenile 18 salmon.
19 5. Minimize population losses to diversions within Reach 2B.
20 Fish Habitat Goal 2 21 Provide habitat to facilitate upstream migration of adult Chinook salmon.
22 Objectives 23 1. Provide opportunities for resting/refuge pools at appropriate intervals throughout 24 Reach 2B.
25 2. Improve habitat conditions (suitable depth and velocity) that support successful 26 upmigration.
27 Fish Habitat Goal 3 28 Provide habitat to support native fishes other than salmon.
29 Objectives 30 1. Create habitat conditions to support fish species historically native to Reach 2B
31 2. Modify channel to enhance existing habitat for native fishes at the restoration low 32 flow condition.
33 3. Provide connectivity within the river system to support native fish movements
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 3-5 – October 2012 San Joaquin River Restoration Program
1 Fish Habitat Goal 4 2 Restore in-channel vegetative communities in support of the establishment of an 3 anadromous fishery.
4 Objectives 5 1. Increase, to the extent practicable, freshwater marsh, perennial and seasonal wetlands 6 in the river corridor for the purposes of enhancing slow velocity habitat conditions for 7 fish.
8 2. Promote the development of shaded aquatic riverine habitat (e.g. by including woody 9 riparian species such as sandbar willow (Salix exigua) and buttonbush (Cephalanthus 10 occidentalis)).
11 3. Include sources for instream woody material at the August and February mean water 12 surface elevations to support suitable habitat for juvenile stages of desired fish 13 species.
14 3.3.2 Fish Passage Goals and Objectives 15 The following fish passage goals and objectives are applicable to Reach 2B.
16 Fish Passage Goal 1 17 Provide flow routing and appropriate fish passage conditions at each of these instream 18 structures and potential future structures:
19 • Chowchilla Bifurcation Structure 20 • San Mateo Avenue crossing 21 • Road 10 ½ crossing (as applicable) 22 • Mendota Pool Bypass Bifurcation Structure (as applicable) 23 • Mendota Pool Bypass Fish Screen 24 • Mendota Pool Bypass Fish Barrier (as applicable) 25 • Mendota Pool Bypass Drop Structures (as applicable) 26 • Mendota Dam (as applicable)
27 Objectives 28 1. Develop preferred fish migration routes based on triggers for the range of Restoration 29 Flows, flood releases, and water deliveries along with the associated flow routing.
30 2. Protect migrating juveniles from entering the Mendota Pool for the range of 31 Restoration Flows.
32 3. Direct upstream migrating adults out of Reach 3 and into the Mendota Pool Bypass at 33 the confluence with Reach 3.
34 4. Ensure up and downstream fish passage during migration flows through each 35 bifurcation structure, the grade control structures in the Mendota Pool Bypass, and the
Mendota Pool Bypass and Reach 2B Improvements Project 3-6 – October 2012 Attachment A – Initial Alternatives Evaluation 3.0 Goals and Objectives
1 San Mateo Avenue and Road 10 ½ crossings in terms of appropriate timing and 2 duration, minimum flow depth, maximum velocity, and entrance and exit conditions.
3
Table 3-1 Restoration Area Habitat Goals and Compatible Reach 2B Habitat Goals
Fish Management Plan Habitat Goal Applicability Compatible Reach 2B Habitat Goals Restore a flow regime that (1) maximizes the duration Restoration Provide functional rearing habitat for and downstream extent of suitable rearing and Area juvenile salmon for the purposes of outmigration temperatures for Chinook salmon and transient rearing during outmigration. other native fishes, and (2) provides year-round river habitat connectivity throughout the Restoration Area. Provide adequate flows and necessary structural Restoration Provide functional rearing habitat for modifications to ensure adult and juvenile passage Area juvenile salmon for the purposes of during the migration periods of both spring-run and transient rearing during outmigration. fall-run Chinook salmon. Provide habitat to facilitate upstream migration of adult Chinook salmon. Provide suitable habitat for Chinook salmon holding, Restoration Provide functional rearing habitat for rearing, and outmigration during a variety of water Area juvenile salmon for the purposes of year types, enabling an expression of a variety of life transient rearing during outmigration. history strategies. Suitable habitat will encompass appropriate holding habitat, spawning areas, and seasonal rearing habitat. Provide water-quality conditions suitable for Chinook Restoration Provide functional rearing habitat for salmon and other native fishes completing their life Area juvenile salmon for the purposes of cycle without lethal or sublethal effects. transient rearing during outmigration and suitable conditions for upstream migration of adults. Reduce predation losses in all reaches by reducing Restoration Provide habitat to support native fishes the extent and suitability of habitat for nonnative Area other than salmon and design fish predatory fish. passage structures to minimize habitat supporting non-native predatory species. Restore habitat complexity, functional floodplains, Restoration Provide functional rearing habitat for and diverse riparian forests that provide habitat for Area juvenile salmon for the purposes of spawning and rearing by native resident species transient rearing during outmigration during winter and spring. and to support other native species. Goal A: Provide flows sufficient to ensure habitat Reaches 2-4 Provide flow routing, fish screens, and connectivity and allow for unimpeded upstream fish passage at current structures and passage and outmigration potential future structures as appropriate. Provide flow routing and fish passage in the river channel. Goal D: Minimize juvenile entrainment losses Reaches 1-5 Provide flow routing and fish passage at current structures and design potential future structures to minimize impediments to migration. Goal F: Eliminate fish passage barriers and minimize Reaches 1-5 Provide flow routing and fish passage migration delays at current structures and potential future structures. Provide flow routing and fish passage in the river channel.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 3-7 – October 2012 San Joaquin River Restoration Program
Table 3-1 Restoration Area Habitat Goals and Compatible Reach 2B Habitat Goals
Fish Management Plan Habitat Goal Applicability Compatible Reach 2B Habitat Goals Goal G: Provide suitable water temperatures for Reaches 2-5 Provide functional rearing habitat for upstream passage, spawning, egg incubation, juvenile salmon for the purposes of rearing, smoltification, and outmigration to the extent transient rearing during outmigration. achievable considering hydrologic, climatic, and Provide habitat to facilitate upstream physical channel characteristics migration of adult Chinook salmon. Goal Q: Ensure suitable quantity and quality of Restoration Provide functional rearing habitat for floodplain and riparian habitat to provide habitat and Area juvenile salmon for the purposes of food resources for Chinook salmon and other fishes transient rearing during outmigration.. Provide habitat to facilitate upstream migration of adult Chinook salmon. Provide habitat to support native fishes other than salmon.
1 Fish Passage Goal 2 2 Provide flow routing and fish passage in the river channel for upstream migrating adults 3 and emigrating juveniles.
4 Objectives 5 1. Encourage the development of channel geometry to provide minimum depth of at 6 least 12 inches through the river thalweg over at least 10 percent of the cross section 7 width during low flow conditions occurring in the migration season.
8 3.4 Habitat Restoration
9 Habitat restoration of Reach 2B of the San Joaquin River would focus on incorporating 10 riparian and floodplain habitat communities (Settlement Paragraph 11(a)(2)) in support of 11 restoring and maintaining a fish population in “good condition” (Settlement Paragraph 2). 12 Adjacent upland habitat communities are also considered important for the long-term 13 health and diversity of the in-stream, riparian, and floodplain communities. Habitat 14 Restoration would consider the natural community structure, function, and capacity for 15 change, within the constraints of flow regulation and other water and land management 16 activities. To the extent feasible, efforts would focus on restoring channel and floodplain 17 processes of water, sediment, and organic matter cycling in the reach. Physical 18 reconstruction would be required to initiate these changes. The altered dynamics would 19 promote ecosystem processes that create and maintain riparian habitats suitable for well- 20 distributed, viable populations of native fish, plants and animals.
21 The key principles for this project begin with restoration of ecosystem processes 22 wherever possible, and restructuring of the new stream channel and floodplain geometry 23 to function under the proposed flow regime. The aim of improving geomorphic function 24 is to benefit long-term ecosystem processes that support native riparian habitats and 25 aquatic species and that promote development of a dynamic, self-sustaining ecosystem to 26 the greatest extent possible.
Mendota Pool Bypass and Reach 2B Improvements Project 3-8 – October 2012 Attachment A – Initial Alternatives Evaluation 3.0 Goals and Objectives
1 Habitat Restoration Goal 2 Encourage the establishment and growth of riparian and floodplain vegetation and habitat 3 complexes and maintain existing vegetation, to the extent practicable.
4 Objectives 5 1. Preserve, to the extent practicable, any remaining patches of functional native 6 vegetation for the purposes of maintaining habitat in Reach 2B while new vegetation 7 becomes established, minimizing short-term project impacts, and supplying 8 propagules for natural vegetation recruitment.
9 2. Restore floodplain habitat by increasing the acreage of riparian woodland, forest and 10 scrub for the purposes of providing multiple benefits to the riparian ecosystem, such 11 as filtering of nutrients and fine sediment, stabilizing channel banks, shading the river 12 channel, and others.
13 3. Include, to the extent practicable, a native vegetative buffer (e.g. upland habitats like 14 valley oak woodland and elderberry savanna) on riparian and floodplain habitats to 15 protect water quality and the health of the adjacent riparian vegetation alliances from 16 chemical drift and other potential external impacts to the health of the fish population.
17 4. Reduce the acreage and distribution of invasive, non-native species (e.g. giant reed- 18 grass (Arundo donax), scarlet wisteria (Sesbania punicea), castor bean (Ricinus 19 communis), and poison hemlock (Conium maculatum)) in order to diminish their 20 range, lessen their competition with native plants, avoid alterations to riparian habitat 21 value and ecosystem function, and protect fish and wildlife.
22 5. Restore a riparian corridor with improved ecological functioning, increased 23 longitudinal connectivity, increased average width of riparian vegetation on both 24 sides of the river, and larger, contiguous patches of woody riparian vegetation and 25 instream woody material.
26 3.5 Seepage
27 Seepage goals and objectives are included to address the prevention of damage or losses 28 to agricultural land outside the Project area. Increased water levels in the Project area as a 29 result of Restoration Flows may have a negative effect on the production value of 30 adjacent lands due to the corresponding increase in water table. These effects would be 31 assessed and addressed as part of the Project according to the goals and objectives. The 32 recommended objectives should be treated as preliminary recommendations, recognizing 33 they would very likely be revised as more is learned about the local seepage needs and 34 additional groundwater modeling, water level, and other data are analyzed to better 35 quantify thresholds.
36 Seepage Goal 37 The Program Environmental Impact Statement/Environmental Impact Report (PEIS/R) 38 states that an objective of the SJRRP is to reduce or avoid adverse or undesirable
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 3-9 – October 2012 San Joaquin River Restoration Program
1 groundwater seepage impacts (SJRRP 2011a). The SJRRP Draft Seepage Management 2 Plan (SJRRP 2011b) describes the monitoring and operating guidelines for the reduction 3 or avoidance of potential seepage-related effects.
4 Objectives 5 1. During the growing season, avoid impacts to crops from water logging by conforming 6 to the minimum depth to water thresholds developed in the Draft Seepage 7 Management Plan (SJRRP 2011b).
8 2. Avoid impacts to crops from salinity by conforming to the maximum soil salinity 9 concentration developed in the Draft Seepage Management Plan (SJRRP 2011b).
10 3. Prevent any significant levee stability issues from standing water, boils, or piping that 11 may compromise the short- or long-term stability of the levees.
12 3.6 Geomorphology
13 Geomorphology goals and objectives are aimed at balancing the available water and 14 sediment loads with the channel planform, slope, cross sectional dimensions, and 15 vegetation. The dynamic nature of a river system includes both the physical processes 16 and the attributes (or form) that the target aquatic species depend on.
17 The focus of the goals and objectives is to utilize geomorphic processes and develop a 18 plan for long-term (including individual flow events and changes over time) channel, 19 floodplain, levee, and structure stability based upon current and future socio-economic, 20 physical, and biological constraints. An understanding of the fluvial geomorphic 21 processes in the Project area will also inform the potential of the Project to meet the Fish 22 Habitat and Passage and Habitat Restoration goals and objectives.
23 Geomorphology Goal 1 24 Provide for long-term stability of required riverine structures, such as diversions, levees 25 and any bed and bank stabilization measures.
26 Objectives 27 1. Minimize erosion and scour problems, and associated maintenance and cost 28 requirements for management agencies.
29 2. Minimize the risk of potential structural failure due to uncertainties inherent in 30 hydrologic and geomorphic sciences and practices.
31 Geomorphology Goal 2 32 Reestablish a functioning river morphology which, to the extent possible, promotes long- 33 term stability of the river system and which supports fish habitat and passage goals by 34 utilizing hydro-geomorphic processes in conjunction with Restoration Flows.
Mendota Pool Bypass and Reach 2B Improvements Project 3-10 – October 2012 Attachment A – Initial Alternatives Evaluation 3.0 Goals and Objectives
1 Objectives 2 1. Establish the optimum channel and floodplain configuration (morphology) that is 3 consistent with the future flow and sediment supply regimes.
4 2. Incorporate vegetation to the extent possible to protect channel banks, while 5 maintaining the channel and floodplain capacity requirements.
6 3. Provide geomorphic features that support fish management goals for migrating and 7 transient rearing habitats (e.g. side channels, bars, woody debris).
8 4. Enable the establishment and maintenance of diverse bed features (e.g. pools) and 9 channel structure (e.g. large woody debris) through natural processes.
10 5. Promote the establishment of a single-thread, low-flow channel to provide for fish 11 passage through natural processes.
12 6. Promote for periodic inundation of floodplain surfaces at the proper frequency for 13 fish access and transient rearing.
14
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Mendota Pool Bypass and Reach 2B Improvements Project 3-12 – October 2012 Attachment A – Initial Alternatives Evaluation
1 4.0 Pre-Initial Options Analysis 2 Pre-initial options analysis included concepts suggested during the Project scoping 3 meetings and other concepts suggested within the Project team (SJRRP 2010d).
4 Some actions suggested during the scoping process and considered by the Project Team 5 were not retained for inclusion in the Project initial options because they would not meet 6 the project purposes, needs, goals, and objectives. These actions, and associated 7 screening information, are summarized below.
8 • Mitigation for flood impacts: No alterations to flood management operations are 9 included in the Project, and mitigation for flood impacts not associated with the 10 Project are unwarranted. Local flooding conditions would be improved through 11 increased capacity within the channel and floodplain and improved levees. 12 • Evaluation and redesign of the Columbia-Mowry Distribution System including 13 facility access, O&M, pumps, pipelines, and power: Modifications to existing 14 canals, pumps, pipelines, access, and power are limited to those relocations 15 necessary to construct the Project. The Project will not include evaluation or 16 redesign of system components outside of those potentially impacted by the 17 Project. 18 • No interruption of water deliveries: The Project goals and objectives do include 19 accommodating water deliveries up to 2,500 cfs within Reach 2B; however, the 20 ability of Reclamation to perform in delivering the contracted water amounts is 21 outside the Project purpose. 22 • Acquire land to support recreation, tourism, flora, fauna, and groundwater 23 recharge: The purpose of the Project does not include independently supporting 24 recreation, tourism, flora (other than riparian habitat), fauna (other than salmon), 25 or groundwater recharge, so land would not be acquired solely for these purposes. 26 However, opportunities may exist to support these functions in conjunction with 27 or incidental to implementation of the Project, and land acquired to meet the 28 Project purposes, needs, goals, and objectives may also benefit recreation, 29 tourism, flora, fauna, and groundwater recharge. 30 • Shortening channel distance to reduce levee length and reduce maintenance costs: 31 Shortening of the river channel or the bypass alignments is currently not 32 considered due to the considerable negative effects to habitat, geomorphology, 33 and sediment continuity in the reach that would result from shortening, or 34 straightening, the channel. 35 • Installing a cutoff channel before the river bends just downstream of the 36 Chowchilla Bifurcation Structure to reduce flooding toward Hwy 180: No 37 alterations to flood management operations are included in the Project, and 38 mitigation for flood impacts not associated with the Project are unwarranted.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 4-1 – October 2012 San Joaquin River Restoration Program
1 Local flooding conditions could be improved through increased capacity within 2 the channel and floodplain and improved levees. 3 • Installing a wall across the river in Reach 3 just below Mendota Dam and 4 diverting water to Mendota Pool: This action would not meet the purpose and 5 need of the Settlement as it would not provide a bypass around the Pool. 6 • Allow salmon in the Pool and Chowchilla Bypass: The extent to which fish would 7 be screened out of the Pool and Chowchilla Bypass has not been determined at 8 this time. Fish screening, and any benefits that may be provided under future 9 conditions, would be considered in the alternatives evaluation process. 10 • Include provisions to allow for Mendota Dam maintenance: Construction of the 11 Bypass places maintenance of Mendota Dam outside the purpose, need, and scope 12 of this project. 13 • Avoid bifurcation of future flows: The Settlement requires Restoration Flows in 14 Reach 2B and in downstream reaches, but it does not require flood conveyance in 15 Reach 2B, and diversion of flood flows into the Chowchilla Bypass is required to 16 meet existing flood operation guidelines. The flexibility to divert flows away from 17 the Bypass and to the Pool is also required to meet potential Exchange Contract 18 water deliveries; however, Restoration Flows are required in the Mendota Pool 19 Bypass and downstream reaches. 20 • Fish screens in the Pool: This action would not meet the purpose and need of the 21 Settlement as it would not provide a bypass around the Pool. In addition, the 22 maintenance, cost and reliability of fish screens for all Pool connections would be 23 problematic. 24 • Evaluate all alternatives that avoid impacts to wetlands: The extent to which 25 initial options impact existing wetlands has not been determined at this time. 26 Extent of impact to existing wetlands would be considered in the alternatives 27 evaluation process. 28 • Avoid dredging or filling in waters of the United States: Filling in waters of the 29 United States would be minimized to the extent possible and would be considered 30 in the alternatives evaluation process. 31 • Address effects of the Project on Milburn Pond: Addressing the effects of the 32 Project on Milburn Pond is outside of the purpose, need, and scope of this project. 33 • Do not reintroduce salmon in order to protect existing riparian habitat: Existing 34 riparian habitat would be considered in the alternatives evaluation process. Not 35 reintroducing salmon would be contrary to the Settlement. 36 Some additional options exist that were not part of the scoping process, but were also 37 considered by the Project Team and not retained for inclusion in the Project initial 38 options because they would not meet the project purposes, needs, goals, and objectives. 39 These include the following:
40 • Construction of levees to withstand a 200-year flood: Eliminated because existing 41 levees in the Project area are not part of the Lower San Joaquin River Flood 42 Control Project.
Mendota Pool Bypass and Reach 2B Improvements Project 4-2 – October 2012 Attachment A – Initial Alternatives Evaluation
1 5.0 Initial Options Refinement 2 During the concept refinement phase of the Project, some of the initial options were 3 revised, refined, or eliminated from further consideration.
4 5.1 Pre-Evaluation Screening
5 The concepts considered and eliminated from further consideration prior to the 6 alternatives evaluation are described below.
7 5.1.1 Bottomless Arch Culverts 8 Bottomless arch culverts were considered in the Initial Options TM as a potential method 9 of improving the crossing at San Mateo Avenue. However, based upon further 10 consideration it was decided that bottomless arch culverts would be too difficult to 11 implement in the sand bed channel of Reach 2B because the culverts would require 12 substantial undercut for foundation work, the culverts would potentially require a 13 concrete floor to stabilize the structures during high flows, and could have an 14 unacceptable failure rate. In addition, less expensive and equally beneficial options are 15 available (i.e., concrete box culverts).
16 5.1.2 Corrugated Metal Pipe Culverts 17 Corrugated metal pipe culverts were considered in the Initial Options TM as a potential 18 method of improving the crossing at San Mateo Avenue. However, based upon further 19 consideration it was decided that corrugated metal pipe culverts would be difficult to 20 design for the fish passage requirements and they may have a shortened lifespan due to 21 the corrosive nature of the soils in the Project area.
22 5.1.3 Bridge 23 A bridge was considered in the Initial Options TM as a potential type of crossing for the 24 San Mateo Avenue crossing. However, based upon further consideration it was found 25 that both a box culvert crossing and a bridge crossing are capable of meeting the fish 26 passage requirements, but the bridge is significantly more expensive. Therefore, the 27 bridge crossing was eliminated from further consideration.
28 5.1.4 San Mateo Avenue Crossing Removal 29 The Project considered removing the San Mateo Avenue crossing as a means of 30 simplifying fish passage in Reach 2B; however, based upon further review, it was found 31 that Madera County has a public right-of-way to the centerline of the river on the north 32 side, and they would like to maintain access on all their rights-of-way for the landowners. 33 Therefore, the Project has not proposed to remove this crossing.
34 5.1.5 Floodplain Vegetation Types 35 In the Initial Options TM, several floodplain vegetation types were considered: fully 36 grassed floodplain, forested riparian fringe along the river with a grassed floodplain, and
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 5-1 – October 2012 San Joaquin River Restoration Program
1 fully forested floodplain. Based upon further review during concept refinement, the 2 floodplain vegetation concept used in the hydraulics modeling was revised to a mosaic 3 type floodplain habitat including a forested riparian fringe along the river and a mixture 4 of grasslands, scrub, and trees on the floodplain. The mosaic floodplain habitat was more 5 typically found along the river historically and can be found in other parts of the San 6 Joaquin Valley today. The preliminary planting plans also present mosaic floodplain 7 habitats but with forested vegetation where inundation depths and soils are appropriate 8 for tree species. The concept used for the hydraulic modeling and that presented in the 9 preliminary planting plans are considered to be comparable in terms of roughness.
10 5.1.6 Floodplain Recontouring 11 As part of the Initial Options development, recontouring of the entire floodplain to allow 12 inundation of large areas at lower flows was considered. Based upon further review 13 during concept refinement, this concept provided less or similar benefit as the select 14 floodplain grading included in the Project alternatives. Wholesale recontouring would 15 not increase the habitat diversity on the floodplain and thus would not provide increased 16 benefits to fish. However, it would require excavation of much larger quantities of 17 material and thus would increase costs. Wholesale recontouring also has the potential to 18 decrease the area of inundation and cause erosion along the channel. Wholesale 19 floodplain recontouring was therefore eliminated from further consideration.
20 5.1.7 Older Levee Setbacks 21 During concept refinement, the levee alignments presented in the Initial Options TM 22 were refined and revised and one alignment was eliminated: Initial Option FP-1. Initial 23 Option FP-1 was found to not sufficiently meet the Settlement requirements to provide 24 floodplain and riparian habitat in Reach 2B. The other levee alignments were modified 25 to account for property lines, field lines, infrastructure, flow and sediment continuity 26 purposes, and to add a minimum 300-foot buffer, where appropriate, between the channel 27 and levee to protect the levee from lateral channel migration and erosion.
28 5.1.8 Mendota Dam Removal 29 The Fisheries Management Workgroup asked the Project to consider removing Mendota 30 Dam as part of the Fresno Slough Dam Initial Alternative. Based upon further 31 consideration and analysis, it was decided that the Project would not remove the dam 32 because it provides a grade control point between Reach 3 and Reach 2B. Without the 33 dam, the channel base level would be lowered and incision could migrate upstream 34 through Reach 2B. This could jeopardize passage conditions at the structures in the 35 project area such as at San Mateo Avenue and Chowchilla Bifurcation Structure where 36 channel grades would potentially be lowered by up to approximately 4.7 feet and 1.9 feet, 37 respectively, effectively relocating the grade-control point. Lowering the base-level 38 would also eliminate overbank flow during all but the highest flows (Tetra Tech 2011a). 39 Furthermore, structural stability of existing and proposed structures could be 40 compromised by the decreased bed elevations and resulting scour.
41 5.1.9 Channel Grading from Reach 3 to Chowchilla Bifurcation Structure 42 The Technical Advisory Committee requested that the Project consider not constructing 43 grade control structures in the Mendota Pool Bypass channel and that the channel be
Mendota Pool Bypass and Reach 2B Improvements Project 5-2 – October 2012 Attachment A – Initial Alternatives Evaluation 5.0 Initial Options Refinement
1 graded from the confluence with Reach 3 at an appropriate slope. Based upon further 2 analysis, it was found that grading the channel at the equilibrium slope starting at the 3 confluence with Reach 3 would lower the entire Mendota Pool Bypass Channel and 4 Reach 2B channel up to approximately 14.3 feet and 11.7 feet, respectively, and that the 5 new base elevation would require excavation (or result in erosion) all the way up to the 6 Chowchilla Bifurcation Structure, which would serve as a grade control point. 7 Furthermore, it was found that this would leave the Reach 2B channel elevation 8 approximately up to 5.3 feet below the floor elevation of the Chowchilla Bifurcation 9 Structure potentially undermining the structure and presenting a fish passage barrier as 10 well as disconnecting the channel from its floodplain throughout Reach 2B (Tetra Tech 11 2011a). Based upon the necessary structural improvements at the Chowchilla Bifurcation 12 Structure to prevent failure, the fish passage impacts, the significant decrease in 13 floodplain inundation area and frequency, the surplus of cut material for the bypass 14 channel, and water quality/stability concerns from eroding channel bed and banks, this 15 concept was eliminated from further consideration.
16 5.1.10 Floating Picket Weir 17 A floating picket weir was considered in the Initial Options TM as a potential method of 18 providing a fish exclusion barrier at the downstream end of the Mendota Pool Bypass 19 Channel to direct fish into the Bypass. Based upon further consideration, this option was 20 eliminated due to the magnitude of flows expected to be seen at the barrier location and 21 this type of weir not being appropriate for such high flows.
22 5.1.11 Behavioral Barrier 23 Behavioral fish barriers were investigated during the appraisal-level design as a means of 24 providing an exclusion/directional barrier at the downstream end of the Mendota Pool 25 Bypass Channel to direct upmigrating adult salmon into the bypass channel and away 26 from the base of Mendota Dam. A system to reroute irrigation flows from Mendota Dam 27 to downstream of the barrier would be included with this concept, leaving slack water 28 between the end of the bypass channel and the Dam. Behavioral barrier systems are a 29 developing technology, but two main types of barriers have been implemented on other 30 rivers: electric barriers and acoustic barriers. Both types of barriers have significant 31 draw-backs for implementation in the Project.
32 Electric barriers generate an electric current through the water across a channel in order 33 to deter fish. Based on existing and previous installations, electric barriers were found to 34 present potential unavoidable electric shock hazards for fish (target and non-target 35 species), other animals, people, and watercraft. Often target fish species either made it 36 past the barrier or were killed. Velocities and depths need to be consistent for the barrier 37 to be effective; something that has proven difficult on reaches with moveable beds and 38 those with variable flows. Velocities also need to be sufficient to sweep stunned fish out 39 of the barrier, which may be difficult in the low slope, low velocity Reach 3. Some 40 programs are considering replacing their electric barriers with different technologies. For 41 all these reasons, the electric barrier is not recommended.
42 Acoustic barriers use a sound signal contained in a bubble curtain of air to deter fish; 43 acoustic barriers may also incorporate the use of strobes and lights to deter fish. There
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 5-3 – October 2012 San Joaquin River Restoration Program
1 are few existing installations of acoustic barriers, but they have been found to be most 2 effective on juvenile fish with minimal effectiveness on adult fish. Effectiveness has also 3 been found to decrease with increasing flows. Acoustic barrier technology is not capable 4 of functioning during high flows such as flood releases from Pine Flat routed down 5 Fresno Slough into Reach 3 (typically at 4,500 cfs or reach capacity). These high flows 6 occur on an average annual frequency of 1 in 5 years, typically in wet years. Since the 7 purpose of the Mendota Pool Bypass Barrier is to direct adult migrating salmon into the 8 bypass at all flows, including flood flows, the acoustic barrier is not recommended.
9 5.1.12 Velocity Barrier 10 Based on design and hydraulic analyses, a velocity barrier at the downstream end of the 11 Mendota Pool Bypass Channel was eliminated from further consideration because the 12 resulting barrier would be higher than Mendota Dam, would increase the elevation in 13 Mendota Pool between 4 and 5 feet, and would necessitate improvements to all levees on 14 Mendota Pool and Fresno Slough.
15 5.1.13 Other Types of Fish Screens 16 During the appraisal-level design several types of fish screens were reviewed for their 17 applicability to the Project for screening fish from the 2,500 cfs diversion to Mendota 18 Pool. The following screen design types were eliminated from further consideration due 19 to design constraints. Horizontal flat plate screens (patented by Farmers Irrigation 20 District, OR) were eliminated because they are intended for use with smaller diversions 21 (less than 100 cfs); there are no physical model studies or field applications 22 demonstrating that this design is capable of handling larger diversions. Travelling 23 screens were eliminated because maintenance is a significant problem, and there are no 24 known field applications for diversions of the Project’s size. Box screens were 25 eliminated because, while they can be sized for larger applications, they function very 26 similarly to cylindrical screens which were considered further. Pump screens were 27 eliminated because they are only applicable to very small diversions (less than 10 cfs). 28 Rotary drum screens were also reviewed but would not provide increased benefits (on- 29 canal installation) and would have higher costs than the selected design (fixed flat plate in 30 “V” configuration). Other fish screen types that may be considered further include: 31 vertical flat plate, inclined flat plate, cone, and cylindrical screens.
32 5.1.14 Pump Diversion to Mendota Pool 33 All the proposed alternatives divert water to Mendota Pool via gravity. During the 34 appraisal-level design, a pump diversion was also considered and preliminary costs were 35 developed. The pump diversion was eliminated from further consideration because the 36 capital improvement costs are nearly four times the cost of the gravity diversions. In 37 addition, the pump diversion would rely on Mendota Dam or another barrier to form a 38 backwatered pool, so the pump diversion would not be able to eliminate the need for a 39 fish passage structure.
Mendota Pool Bypass and Reach 2B Improvements Project 5-4 – October 2012 Attachment A – Initial Alternatives Evaluation 5.0 Initial Options Refinement
1 5.2 Other Refinements
2 Many concepts were refined or revised during appraisal-level design before moving into 3 the alternatives evaluation; those refinements are described below.
4 5.2.1 Levee Alignments 5 During the concept refinement, a minimum 300-foot buffer between the channel and 6 levee to protect the levee from lateral channel migration and erosion was included on all 7 levee alignments. However, at Bend 10 (approximately RM 209), the river channel and 8 existing right bank levee are located directly adjacent to the Columbia Canal. Providing 9 the 300-foot buffer on this bend would require relocating the Columbia Canal. As an 10 alternative, the Project considered building the new levee along the existing right bank 11 levee alignment and providing revetment along the bend to protect the levee. Revetment 12 is not desirable from a habitat and fisheries perspective. A preliminary cost comparison 13 was prepared to compare the construction and land acquisition costs for the 300-foot 14 buffer versus the revetment on Bend 10. Based on the preliminary cost comparison, it 15 was decided that both bank protection methods at Bend 10 would be evaluated as options 16 in the alternatives evaluation (see Section 7.4.1).
17 5.2.2 Floodplain Grading 18 During concept refinement, the inclusion of floodplain grading was considered as a 19 means of providing greater variety of inundation depths on the floodplain as well as more 20 inundation at lower flows. Several iterations of grading were analyzed: 1-2 feet of 21 excavation to create 3-4-foot water depths on the floodplain during most floodplain 22 inundation flows, then approximately 1 foot of excavation on certain inside bends to 23 create 3-4 water depths on the floodplain, and finally approximately 1 foot of excavation 24 to provide high-flow channels and connectivity across certain bends in the floodplain. In 25 the first two iterations of grading, the analysis showed that the additional capacity 26 generated in the excavated areas reduced the area of floodplain inundation and did not 27 increase the variety of inundation depths on the floodplain. The loss of floodplain 28 inundation acreage led to the iterative decrease in the quantity of grading until the high- 29 flow channel concept was selected for inclusion in the design. The high-flow channels 30 do not significantly affect inundation acreages or the variety of inundation depths, but 31 they may provide other fisheries benefits such as juvenile rearing and food production as 32 well as inundation at lower flows.
33 5.2.3 Removal of Existing Levees 34 Removal of existing levees is necessary to expand the inundation area of the floodplain 35 out to the proposed levees. Rather than remove existing levees in their entirety, a 36 preliminary plan to selectively preserve some levees was developed based upon the 37 locations of highly desirable existing vegetation (native and sensitive vegetation 38 communities that can serve as seed banks for future vegetation communities) as well as 39 hydraulic performance of the channel and floodplain. Where levee removal was 40 necessary to allow inundation of the floodplain and floodplain connectivity for fish 41 movement, vegetation and levee preservation was not included in the design.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 5-5 – October 2012 San Joaquin River Restoration Program
1 5.2.4 Placement of Structures 2 During concept refinement, the placement of the bifurcation control structures at the head 3 of the Mendota Pool Bypass Channel was refined. For the Settlement alignment of the 4 bypass (see description in Section 7.2.2), the Mendota Pool control structure was 5 relocated downstream of the confluence with Reach 2B so that unfarmable land to the 6 south of the confluence could be incorporated as floodplain.
7 5.2.5 Operational Flexibility 8 During concept refinement, it was decided that the structure designs and fish routing 9 needed to function with full operational flexibility. Meaning that fish passage facilities 10 were selected and designed based on their ability to fully function and route fish through 11 the Mendota Pool Bypass facilities during both of the following operational scenarios:
12 • Zero to 4,500 cfs through the Mendota Pool Bypass facilities with no diversion to 13 Mendota Pool 14 • Zero to 2,500 cfs into the Mendota Pool and the remainder of Reach 2B flows 15 through the Mendota Pool Bypass facilities simultaneously 16 Not all types of fish passage facilities are capable of operating under such variable flow 17 and hydraulic head conditions, and the flexibility required necessarily limited the types of 18 facilities and structures that are feasible for the project.
19 5.2.6 Fish Passage Design Criteria 20 The Project team worked in conjunction with the Fisheries Management Workgroup and 21 other experts at the fisheries agencies to develop criteria for fish passage that were used 22 to design structures and analyze passage conditions in the channel and at structures 23 during the concept refinement phase. The design criteria are structured around the life 24 stages of the target anadromous species and the timing of the runs for upstream 25 movement of adult fall and spring run Chinook and winter steelhead and the upstream 26 and downstream movement of juvenile life stages spawned from these runs. 27 Recommended criteria are based on a combination of swimming ability of the fish 28 species as reported in scientific papers and criteria in agency design guidelines. 29 Recommended design criteria to provide for successful fish passage (depth of flow, 30 suitable velocity ranges and jump height) are provided in Table 5-1. The design criteria 31 for a particular species would be met over the associated flow range (minimum flow to 32 maximum flow).
33
Mendota Pool Bypass and Reach 2B Improvements Project 5-6 – October 2012 Attachment A – Initial Alternatives Evaluation 5.0 Initial Options Refinement
1 Table 5-1. 2 Fish Design Criteria
3
1
2
stage - Depth Depth Species Velocity Migration Migration Maximum Maximum Life Frequency Timeframe Height Jump Minimum Pool Pool Minimum Minimum Flow Minimum Maximum Flow Minimum Water
years cfs cfs fps feet feet feet
Spring and All years 4 5 Adult 115 4,500 4.0 1.2 1.0 fall pulse except CL Late spring Chinook Juvenile All years 6 5 diminishing 125 n/a 1.0 1.0 0.5 salmon (upstream) except CL flows
Juvenile All years 7 5 Nov-May 85 n/a n/a 1.0 n/a (downstream) except CL
Spring and All years 4 5 Steelhead Adult 115 4,500 4.0 1.2 1.0 fall pulse except CL None – Spring W and NW 8 Sturgeon Adult 1,138 4,500 6.6 3.3 swim n/a pulse years through
Spring All years 6 9 9 9 Lamprey Adult 125 4,500 n/a pulse except CL W, NW, None – Other Spring 10 Adult and ND 543 4,500 2.5 1.0 swim n/a native fish pulse years through W = wet; NW = normal wet; ND = normal dry; CL = critical low 1 Recommended velocities are for drop structures or structures with short longitudinal lengths. For structures with longer lengths (e.g., culverts and bifurcation structures under certain conditions), maximum velocities would be based on Anadromous Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage at Stream Crossings (NMFS 2001). 2 Minimum water depth criteria based on 1.5 times body depth or 1 feet depth, whichever is greater. 3 Maximum jump height criteria based on criteria in Anadromous Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage at Stream Crossings (NMFS 2001). 4 Based on Exhibit B lowest flow in the fall spawning period (starts Oct 1) for the desired frequency; all Spring Pulse Flows are higher. 5 Pool depths to be based on criteria in Anadromous Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage at Stream Crossings (NMFS 2001). 6 Based on lowest flow within Exhibit B Spring Pulse Flow period for the desired frequency. 7 Based on lowest flow within desired migration period for the desired frequency. 8 Wet and normal wet years constitute 50% of years in the historical record. Based on an analysis of varying Restoration Flows management strategies (Reclamation 2010); flows with a 50% exceedance could range from 1,138 to 4,500 cfs. 9 Lamprey designs to be based on criteria in Best Management Practices for Pacific Lamprey (USFWS 2010) 10 Wet, normal wet, and normal dry years constitute 80% of years in the historical record. Based on an analysis of varying Restoration Flows management strategies (Reclamation 2010); flows with an 80% exceedance could range from 543 to 4,500 cfs. 3
4 5.2.7 Columbia Canal Relocation Facilities 5 The Bypass Initial Alternatives will require modification and relocation of portions of the 6 conveyance facilities for the Columbia Canal Company (CCC). Currently, irrigation 7 water is diverted into an inlet channel approximately 6,000 feet upstream from the 8 Mendota Dam, which backwaters Mendota Pool and the inlet channel, where it is 9 pumped by Reclamation’s Main Columbia Pumping Plant. Approximately 125 cfs of 10 irrigation water is diverted to the west Columbia Canal and 125 cfs into a concrete lined
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 5-7 – October 2012 San Joaquin River Restoration Program
1 ditch to the east. The location and level of impact to the CCC facilities depends on the 2 Bypass Initial Alternative. Generally, either the alternative cuts across the CCC or 3 disconnects it from the Mendota Pool.
4 The Settlement Alignment Initial Alternative will sever portions of the Columbia Canal 5 south of the Settlement Alignment from the remainder of the canal system. This 6 necessitates relocating a portion of the canal and installing siphons to pass irrigation flow, 7 from the existing USBR Main Columbia Pumping Plant, beneath the bypass channel to 8 the irrigation canals. The pre-appraisal designs include installing two siphons to allow 9 irrigation flows to pass beneath the upstream and downstream ends of the Settlement 10 Alignment. This would allow the use of the existing canal to the south of the bypass 11 channel to continue to convey irrigation water. This design was revised for appraisal 12 design by including a double barrel siphon on the upstream end of the bypass channel, 13 and a realigned canal just north of the bypass channel. It was determined that agricultural 14 lands to the south between the bypass channel and river would likely no longer receive 15 irrigation deliveries from the CCC, making the two siphon design more costly and 16 inefficient. The future detailed design phase may consider including pumps and 17 pressurized pipes to convey water from Mendota Pool to the CCC as a means of avoiding 18 sediment build-up in the siphons and to mitigate for possible fluctuations in the Pool 19 water surface level.
20 The Compact Alignment Initial Alternative will prevent the use of the existing CCC inlet 21 channel and Pumping Plant. The pre-appraisal and appraisal designs are essentially the 22 same. The Pumping Plant will be relocated to the Mendota Pool about 1800 feet 23 upstream of the Dam. Water will be pumped under the bypass channel via pipe and into 24 the Columbia Canal. Water will be diverted to the east or west into irrigation canals 25 using a new outlet structure. The outlet structure and the canal to the east will need to be 26 raised to allow water to be diverted in both directions. The inlet location for the appraisal 27 design was moved approximately 800 feet southeast from the pre-appraisal location due 28 to the original location being a shallow area of the river.
29 The Fresno Slough Dam Initial Alternative will prevent the use of the existing CCC inlet 30 channel and Pumping Plant. For this alternative, four different designs were developed to 31 account for the different Reach 2B Floodplain Initial Alternatives and water delivery 32 canal options. All four designs were basically the same, but the layouts are slightly 33 different to account for the levees and water delivery canals. In general, a new pump 34 station would be located on Mendota Pool as created by the proposed Fresno Slough 35 Dam, and irrigation water would initially be diverted to canals on the south side of the 36 river. The water would travel by gravity in the canal, then into pipeline siphons under the 37 river, and then be pumped again into the Columbia Canal where it is diverted to the west 38 or east. The easterly portion of the Columbia Canal would need to be raised and 39 modifications would be made to various sections of existing canals to allow the majority 40 of the canals to be gravity fed.
41 5.2.8 Fresno Slough Dam Height 42 During concept refinement it was decided that the proposed height of the Fresno Slough 43 Dam would be the same height as the existing Mendota Dam and not the height of the
Mendota Pool Bypass and Reach 2B Improvements Project 5-8 – October 2012 Attachment A – Initial Alternatives Evaluation 5.0 Initial Options Refinement
1 proposed Mendota Dam, which is being considered as part of a separate project for the 2 Mendota Wildlife Refuges. Using the existing Mendota Dam height is consistent with 3 the other Bypass Initial Alternatives (Settlement and Compact alignments), neither of 4 which would raise the height of Mendota Dam.
5 5.2.9 Picket Barriers 6 In addition to the review and exclusion of behavioral barriers and velocity barriers 7 described in Sections 5.1.10 and 5.1.12, hydraulic analyses were performed on several 8 picket barrier concepts during concept refinement:
9 • Picket barrier across the Reach 3 channel designed for 600 cfs through the 10 structure (from Mendota Dam) and 4,500 cfs in the downstream channel 11 • Picket barrier across the Reach 3 channel designed for 4,500 cfs through the 12 structure (from Mendota Dam) and 4,500 cfs in the downstream channel 13 • Picket barrier across the Reach 3 channel and floodplain designed for 4,500 cfs 14 through the structure (from Mendota Dam) and 4,500 cfs in the downstream 15 channel 16 The skew angle of the structure to the direction of flow was also refined, concepts for the 17 alignments of extension levees were developed, and preliminary costs for levee 18 improvements along Reach 3 between the Mendota Dam and the barrier were developed. 19 The picket barrier across the channel and floodplain (third option) was selected for 20 evaluation because it does not restrict the flow width or floodplain processes.
21 5.2.10 Infrastructure Relocations and Floodproofing 22 During concept refinement it was decided that relocation of the three City of Mendota 23 wells located on the south side of the river would not be included in the costs of 24 floodplain alternatives where the wells are inside the levee alignments. These wells are 25 deep, and were difficult to drill and site when installed, so relocation of these wells could 26 result in significant costs. The design of the Initial Alternatives includes costs to raise the 27 wells and construct an access road across the floodplain.
28 5.2.11 Seepage Mitigation 29 At the time of the appraisal-level design there was minimal geotechnical information 30 available to determine the potential location, extents, and duration of nuisance seepage 31 resulting from the Restoration Flows. In addition, the CVHM-SJR model results were 32 not available. A preliminary, cross-section based groundwater model was developed to 33 determine the approximate extent of nuisance seepage. As a result, the design of the 34 Initial Alternatives assumes that slurry walls will be installed along the entire length of 35 the proposed levees, except along lands not sensitive to increased groundwater elevations 36 (e.g. natural ground and grazing lands). It is expected that the type, length, and design of 37 seepage mitigation measures will be refined once geotechnical data and the CVHM-SJR 38 model results become available.
39
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Mendota Pool Bypass and Reach 2B Improvements Project 5-10 – October 2012 Attachment A – Initial Alternatives Evaluation
1 6.0 Initial Alternatives Evaluation Criteria 2 The criteria described below were determined for each of the Initial Alternatives 3 described in Section 7.0. Criteria for the Floodplain Initial Alternatives and Bypass 4 Initial Alternatives (including applicable structures) were determined independently so 5 that the Floodplain Initial Alternatives could be scored amongst themselves and likewise 6 for the Bypass Initial Alternatives. The intent was to allow any Floodplain Initial 7 Alternative to be combined with any Bypass Initial Alternative during development of the 8 Final Alternatives without the need to evaluate all possible combinations. For the 9 purposes of the evaluation, the location of the junction between the Floodplain Initial 10 Alternatives and the Bypass Initial Alternatives needed to be the same for all Initial 11 Alternatives to allow the independent scoring. The Floodplain Initial Alternatives extend 12 from the Chowchilla Bifurcation Structure downstream to the location of the head of the 13 Settlement Alignment Bypass, and the Bypass Initial Alternatives extend from the 14 location of the head of the Settlement Alignment Bypass downstream to their respective 15 tie-in locations in Reach 3.
16 6.1 Implementation/Technical Feasibility
17 The sections below describe the criteria chosen to represent the range of implementation 18 and technical feasibility of the Initial Alternatives.
19 6.1.1 Costs
20 Capital Improvement Costs 21 Capital improvement costs include the costs to procure and manage contractors, buy and 22 haul materials, do earthwork, build structures (including concrete, metal, valves, 23 equipment, plumbing, electrical, power, and communications work), and stabilize and 24 revegetate (plant and irrigate) the Project. Capital improvement costs do not include land 25 acquisition, mitigation, or operations, repair, and maintenance costs.
26 Construction costs are the combined cost of contractor payments and construction 27 inspection/administration. Contractor payments were estimated by itemizing the contract 28 bid items and applying current labor and materials rates to develop the costs for each bid 29 item.
30 Costs were based on 2007 labor, equipment, and material rates, estimated time for 31 equipment, and the quantity estimates using Reclamation Cost Estimating guidelines. 32 Unit costs were also developed by Provost and Pritchard Engineering, Tetra Tech, and 33 DWR (equipment costs based on 2007 Caltrans rates). Final costs were subject to 34 rounding and contingencies as outlined in the USBR March 1989 “Cost Estimating 35 Handbook.”
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-1 – October 2012 San Joaquin River Restoration Program
1 Land Costs 2 Data from the ASFMRA was reviewed with information on the number of acres of each 3 crop that will be permanently removed from production. The average land cost was 4 found to be somewhat less than $10,000 per acre, so a more conservative estimate of 5 $10,000 per acre (independent of crop type) was chosen for the appraisal-level design and 6 alternatives evaluation. The purpose of selecting the land cost was solely to provide a 7 consistent value to evaluate the relative acquisition costs associated with the various 8 Initial Alternatives. It is not meant to represent land values that will be determined as 9 part of the real estate appraisal process in a later phase of the Project
10 Operation and Maintenance Costs 11 Operation and maintenance costs include annual power costs, annual equipment 12 maintenance cost, including periodic replacement, annual structure maintenance costs, 13 and annual vegetation management maintenance costs. More specifically, levee 14 maintenance includes vegetation management, access roads, levee inspections, levee 15 restoration, rodent control, minor structures, encroachment removal, levee patrolling 16 during flood events, and equipment costs. Floodplain maintenance includes vegetation 17 management for invasives and periodic floodplain and channel shaping to retain capacity. 18 There are no operating costs for levees or floodplains.
19 San Mateo Avenue maintenance includes post-overtopping flow and annual maintenance 20 to keep the crossing functional, which includes cleaning debris or sediment from culverts, 21 clearing debris from the roadway after flows have receded, and repairing or replacing 22 minor structures. The crossing is assumed to be equipped with manually locking gates to 23 prevent traffic crossing during overtopping flows. Operations costs assume the road 24 would be closed once a year, in the late fall, and open in the late spring.
25 Bifurcation Structure maintenance includes annual operating maintenance for radial 26 gates, lubing the fittings, replacing seals, greasing and inspecting the motors, and 27 cleaning the trash rack. Operating costs include operating the motors for the radial gates, 28 inspection and assessment of the gates, and adjusting the gates for various stages of 29 flows.
30 Fish ladder maintenance and operations costs include periodic monitoring of the fish 31 ladder for debris and minor cleaning.
32 Fish screen maintenance includes pre and post operating maintenance for screens 33 (periodically removing, cleaning, and replacing screens), brush cleaning system (periodic 34 repair or parts replacement, inspections, and grease motor), and trash rack (periodic 35 repair or parts replacement, inspections, and grease motor). Screen operations assume 36 daily operations during juvenile migration periods during Pool deliveries. Operations 37 costs include visual inspection, flow verification, clearing obstructions and debris, 38 adjusting the baffles, permitting and regulatory compliance, velocity measurements, 39 performance estimate, and power.
40 Fish barrier operations assume daily operations during adult migration period. Operations 41 costs include visual inspection, flow verification, and clearing obstructions and debris.
Mendota Pool Bypass and Reach 2B Improvements Project 6-2 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 Seasonal operations include installation and removal of the barrier and permitting and 2 regulatory compliance.
3 Water delivery canals are either an unlined earthen channel or concrete lined. 4 Maintenance costs of the unlined earthen channel include sediment removal and channel 5 re-shaping. Maintenance costs of the concrete lined channel include sediment removal. 6 There are no operating costs for the water delivery canal.
7 Fresno Slough Dam maintenance costs include annual operating maintenance for radial 8 gates, lubing the fittings, replacing seals, greasing and inspecting the motors, and repair 9 of miscellaneous equipment. Operating costs include operating the motors for the gates, 10 motor for the automatic trash sweep, and annual permitting fees.
11 Costs were based on 2007 labor, equipment, and material rates, estimated time for 12 equipment, and the quantity estimates using Reclamation Cost Estimating guidelines. 13 Unit costs were also developed by Provost and Pritchard Engineering, Tetra Tech, and 14 DWR (equipment costs based on 2007 Caltrans rates). Final costs were subject to 15 rounding and contingencies as outlined in the USBR March 1989 “Cost Estimating 16 Handbook.” Additional costs were estimated for environmental permitting for work to be 17 completed as previously discussed. This was calculated to be a bulk sum of salary and 18 overhead.
19 Evaluation Criteria 20 • Capital improvement costs: The costs associated with designing and building the 21 Initial Alternative in total dollars. 22 • Land costs: The estimated cost of land expected to be purchased for the Initial 23 Alternative based on an average approximate value of $10,000 per acre. 24 • Operation and maintenance costs: The annual dollars required to operate and 25 maintain the Initial Alternative.
26 Criteria initially identified but not evaluated 27 Other criteria were initially identified in the Analyitical Tools TM (SJRRP 2010f) for 28 evaluating the costs of the Project. These criteria were removed for the reasons described 29 below.
30 • The Project was considered to be too early in the process for thoughtful and 31 reasonable development of mitigation needs, ratios, assessment of potential ways 32 to meet mitigation and monitoring requirements. Mitigation costs were, therefore, 33 removed from the evaluation. However, because mitigation would likely be 34 proportional to environmental effects the relative differences in likely mitigation 35 alternatives are captured in the environmental effects criteria for the purpose of 36 comparison.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-3 – October 2012 San Joaquin River Restoration Program
1 6.1.2 Time to Build
2 Construction 3 Labor and equipment time and hourly rates and construction quantities were estimated for 4 each activity and sub-activity during construction. Activity schedules are based on 5 finish-start logic with no overlap in sub-activities. Main activities are scheduled based on 6 finish-start logic with a negative 50% lag between each main activity and the subsequent 7 main activity. Labor and equipment rates include 15% markup. Production rates are 8 based on 8 hour shifts. Schedule based on an average of 21 working days per month (252 9 working days per year).
10 Evaluation Criteria 11 • Time until action is functional: the number of months to construct and plant 12 restoration vegetation for the Initial Alternative.
13 Criteria initially identified but not evaluated 14 Other criteria were initially identified in the Analyitical Tools TM (SJRRP 2010f) for 15 evaluating the costs of the Project. These criteria were removed for the reasons described 16 below.
17 • Design costs are included as a percent contingency in the capital improvement 18 costs, but the design timeline was not estimated, so this criterion was removed 19 from the evaluation. 20 • Permitting timelines are assumed to be independent of which alternative is 21 selected, so this criterion was removed from the evaluation.
22 6.2 Objectives/Benefits Achievement
23 The sections below describe the criteria chosen to represent the range of objectives and 24 benefits achievement offered by the Initial Alternatives.
25 6.2.1 Flow Conveyance 26 Since all Initial Alternatives have the ability to convey up to 4,500 cfs along the path of 27 Restoration Flows and to divert up to 2,500 cfs to the Mendota Pool, this criterion was 28 not a differentiator and was removed from the evaluation.
29 6.2.2 Fish Habitat and Passage 30 The discussion below provides background information and documentation of the 31 approach used in evaluating fish habitat and passage. Fish habitat in the three Bypass 32 Initial Alternatives is evaluated separately from that associated with the Floodplain Initial 33 Alternatives.
34 Floodplain Fish Habitat 35 The assessment of floodplain habitat in California is founded in the concept of the 36 floodplain activation flow (FAF) (Williams 2009 and Opperman 2010). The FAF is 37 considered the minimum flood pulse necessary to trigger or “activate” floodplain
Mendota Pool Bypass and Reach 2B Improvements Project 6-4 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 ecological processes within an alluvial system. The flow, which allows hydraulic 2 connectivity between the river and floodplain, must occur for a suitable duration and 3 occur with a great enough frequency to assure that ecological benefits are meaningful. 4 The FAF is defined as the river stage that is exceeded in at least two out of three years 5 and sustained for at least seven days from mid-March to mid-May (Williams 2009).
6 As defined, the FAF has a season that is based on work conducted on the Sacramento 7 River, and it is likely appropriate for the San Joaquin River as well. While the FAF, as 8 defined, may function for sediment delivery, water recharge, and seed dispersal, it is not 9 sustained for a sufficient period of time to provide a meaningful support of juvenile 10 salmon rearing; however, even short-term floodplain inundation can provide some 11 benefits for salmon. In order to function for fish habitat and increase juvenile growth 12 rates, the flows would need to be a sustained for longer than seven days and/or provide 13 repeat inundation periods during the mid-March to mid-May period.
14 Dramatic differences have been shown in growth rates of juvenile Chinook salmon reared 15 on vegetated floodplains versus those reared in the channel downstream of those 16 floodplains over a period of 54 days (Jeffres 2008 and as cited in Opperman 2010). The 17 juvenile salmon outmigration on the San Joaquin River is anticipated to occur between 18 about March 15 to May 15. Reach 2B is not adjacent to, or near any spawning habitat, so 19 juveniles using this reach would likely be migrating downstream toward the ocean, 20 which is a life history stage referred to as transient rearing and also described as a “grow 21 as you go” life stage. For this outmigration period, an inundated floodplain could provide 22 additional valuable transient rearing habitat.
23 Furthermore, based on an analysis of potential future Restoration Flow management 24 strategies, it appears that flows with a 2 out of 3 year recurrence interval, as described by 25 the FAF, would not inundate much of the Reach 2B floodplain. The flows at this annual 26 frequency generally remain in the channel. Geomorphologically speaking, flows that 27 recur on a 2 of 3 year basis are often described as the “channel forming flow”, and it is 28 not expected that a flow of this frequency would inundate the floodplain. Therefore, a 29 less-frequent flow, which would inundate the floodplain, with a longer duration was 30 developed to support the evaluation of fish habitat.
31 Floodplain Salmonid Rearing Activation Flow 32 For the purpose of this evaluation, a Floodplain Salmonid Rearing Activation Flow 33 (FSRAF) was defined based on the characteristics of functional floodplain for juvenile 34 salmonid rearing. The FSRAF is assumed to be the minimum flow needed to support 35 floodplain rearing habitat for juvenile salmonids in Reach 2B and is established as the 36 flow that is sustained for 20 days between March 15 and May 15 and has a frequency of 1 37 out of 2 years. The FSRAF for Reach 2B inundates the floodplain directly connected to 38 the main channel. For Reach 2B, the FSRAF is estimated as 2,300 cfs based on a 39 frequency-duration analysis of potential future Restoration Flow management strategies
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-5 – October 2012 San Joaquin River Restoration Program
1 (SJRRP 2010a)1. The FSRAF should not be interpreted as a recommendation for 2 managing flows in the San Joaquin River; it is the flow that creates sufficient floodplain 3 habitat in Reach 2B for a sufficiently long duration to provide a benefit for rearing young 4 salmon.
5 The evaluation of the Floodplain Initial Alternatives assumes that the hydrologic criteria 6 of the FSRAF are achievable in Reach 2B under the Restoration Flows. While specific 7 hydrographs of the Restoration Flows are not defined at this time, a framework study was 8 completed that incorporates the management of the volume of water reserved for the 9 Restoration Flows (SJRRP 2010a). The actual flows will be recommended by the 10 Restoration Administer with input from the Technical Advisory Committee. Actual 11 flows cannot be predicted with any degree of certainty at this time because the 12 Restoration Administrator must also consider reservoir conditions and precipitation 13 updates and predictions as well as a variety of goals and purposes before flows are set, 14 including the consideration of the value of channel forming flows, riparian recruitment 15 flows, and fish flows not only in Reach 2B but also in other reaches of the river. Given 16 the uncertainty surrounding actual flow conditions, the evaluation of the Floodplain 17 Initial Alternatives focused on floodplain inundation (modeled depths and velocities and 18 area of inundation) for steady state flows of 2,000, 2,500, 3,000 and 4,500 cfs, and the 19 2,500 cfs inundation was used as surrogate for the 2,300 cfs FSRAF.
20 The Floodplain Initial Alternatives were evaluated based upon their potential to support 21 juvenile salmon transient rearing with the assumption that this habitat would also provide 22 habitat for other native fishes. The timing, in early spring, for salmon rearing habitat and 23 native fish spawning is similar as native fishes tend to spawn earlier in the year when 24 water temperatures are relatively cool. In contrast, floodplain inundation late in the 25 spring or early summer is not as favorable to salmon and native fishes when conditions 26 are more in line with the time period and temperature for the reproduction of non-native 27 fish (Crain 2004). Therefore, the March 15 to May 15 inundation period is the preferred 28 time frame for floodplain inundation within Reach 2B.
29 Shallow Water Habitat Quality 30 Juvenile salmon rearing habitat is evaluated for direct rearing which is defined as areas 31 with water greater than 1.0 feet deep. This is habitat that juvenile salmon occupy and use 32 as they forage on the floodplain. Primary production2 occurs in water that is less than a 33 foot deep. This is habitat that salmon do not directly occupy but does produce algae, 34 zooplankton and aquatic macroinvertebrates or other larval fishes that then become food
1 This was done for the daily flow record from March 1, 1922 to February 29, 2008. Each year, only the time period of March 15 – May 15 was assessed. A 20-day running window was applied to the data set, and the minimum (sustained) flow was counted as the flow value for that entire 20-day window. The maximum of these sustained flows each year was then ranked, and the flow that was exceeded in one half of all years was identified to find the flow that occurs in approximately one out of two years with duration of 20 days between March 15 and May 15. 2 Primary production in aquatic systems refers to the production of bacteria, diatoms and algae or other vegetation components that then drive the production of invertebrates that become food for fish on the floodplain or in the river.
Mendota Pool Bypass and Reach 2B Improvements Project 6-6 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 for salmon on the remainder of the floodplain or in the main channel. While floodplain 2 areas with depths less than 1.0 feet may provide some resources used by salmon, 3 extensive areas of very shallow water (less than 0.5 feet deep) do not provide direct 4 benefit to rearing salmon since these areas would be isolated from the flowing deeper 5 waters used by salmon. However, a floodplain that does not have enough shallow water 6 may not provide sufficient primary production to support salmon.
7 Large expanses of very shallow water habitat would not provide a lot of value to fish 8 using the floodplains. The very shallow water habitats would have low velocities 9 resulting in limited mixing with water adjacent to the rearing habitat. Food resources 10 produced in these areas would not contribute to overall productivity in the river. As the 11 flood levels recede, much of this habitat, especially on the south side of the channel 12 where it is so prevalent, would disconnect from the rearing habitat and the channel.
13 Guidelines are not forthcoming in the literature regarding the ideal proportion of shallow 14 to deep water because all floodplain waters are typically considered “shallow water 15 habitat” in the literature. However, logic implies that large expanses of water less than 16 0.5 feet deep would result in very little of the shallow water area exchanging food 17 resources with the rearing habitat on the floodplain because of the limited interaction 18 between the extensive very shallow water and the rearing habitat on the floodplain. 19 Given the physical limitation of transport from shallow water to the deeper floodplain 20 areas or the channel, an optimal width of very shallow floodplain is probably somewhere 21 around 100-200 feet.
22 All the Floodplain Initial Alternatives provide some shallow water habitat at flows of 23 2,300 cfs, but because of the extensive areas of shallow water on the wider floodplain 24 alternatives, much of this habitat is physically distant from rearing habitat and would not 25 benefit the rearing habitat. A method for evaluating the quality of the shallow water 26 habitat was needed to differentiate the relative benefits or lack of benefits associated with 27 each Initial Alternative. A rating system based on the proportion of very shallow water 28 habitat (less than 0.5 feet) to rearing habitat (greater than 1.0 feet) was developed based 29 on literature reviews and professional knowledge. The evaluation does not consider the 30 amount of floodplain habitat between 0.5 and 1.0 feet because this area would be 31 transitional between the very shallow water and rearing habitats. The evaluation 32 considers that too little very shallow water prevents development of sufficient levels of 33 primary production to support fish using the floodplain rearing habitat. In contrast, too 34 much very shallow water habitat results in large areas of primary production that are 35 functionally isolated from the floodplain rearing areas and thus are of minimal benefit to 36 salmon. Since inundation depth is inversely related to floodplain width, a balance 37 between the quantities of these two habitats is needed to provide suitable conditions for 38 juvenile salmon in Reach 2B. The rating system is outlined in Table 6-1.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-7 – October 2012 San Joaquin River Restoration Program
1 Table 6-1 2 Shallow Water Habitat Quality Rating Scale Rating Ratio of Very Shallow Water Habitat (less than 0.5 feet) to Rearing Habitat (greater than 1.0 feet) Poor Less than 0.20 Fair 0.21-0.30 Good 0.31 - 0.40 Fair 0.41 - 0.50 Poor Greater than 0.50
3 Floodplain Modeling 4 For the purposes of the evaluation, the location of the junction between the Floodplain 5 Initial Alternatives and the Bypass Initial Alternatives needed to be the same for all Initial 6 Alternatives to allow the independent scoring. The Floodplain Initial Alternatives extend 7 from the Chowchilla Bifurcation Structure downstream to the location of the head of the 8 Settlement Alignment Bypass, and the Bypass Initial Alternatives extend from the 9 location of the head of the Settlement Alignment Bypass downstream to their respective 10 tie-in locations in Reach 3. The river channel and each Floodplain Initial Alternative and 11 each Bypass Initial Alternative were modeled in HEC-RAS and SRH-2D. The water 12 depth results (from HEC-RAS) and velocity results (from SRH-2D) were output into GIS 13 to calculate the acreages of various depth and velocity ranges associated with each 14 alternative. Specifically, FP-1, FP-2, FP-3, FP-4, and FP-5 were modeled in HEC-RAS 15 at flows of 1,000, 1,500, 2,000, 2,500, 3,000 and 4,500 cfs, and FP-1, FP-3, FP-4, and 16 FP-5 were modeled in SRH-2D at flows of 2,000, 3,000, and 4,500 cfs. The results were 17 also processed graphically to produce “heat maps” of the depth and velocity ranges. 18 Additional processing included overlaying the areas with velocities less than 0.1 fps on 19 the depth maps. However, the velocity results did not substantially differentiate the 20 Initial Floodplain Alternatives, and after a close examination of the data, the velocity data 21 was not used further in the evaluation.
22 Some of the HEC-RAS model runs show inundation occurring in areas disconnected 23 from the river channel. This is an artifact of the HEC-RAS model, and most of these 24 areas were associated with the lower modeled flows. To eliminate this “noise” from the 25 analysis, and knowing that the channel begins to overbank at about 1,800 cfs along the 26 eastern portion of Reach 2B and around 1,200 cfs along the western portion, the fish 27 habitat evaluation only used modeling results for flows greater than 2,000 cfs. Further 28 review of the flows resulted in the FSRAF concept, so Initial Alternatives were evaluated 29 by comparing the amount of acres for 2,500 cfs.
30 In addition, comparison of inundation maps and velocity maps sometimes shows that 31 slightly different areas of the floodplain are subjected to flows. This is an artifact of the 32 different modeling routines in the HEC-RAS and SRH-2D models; the differences were 33 reviewed and considered minor.
Mendota Pool Bypass and Reach 2B Improvements Project 6-8 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 Fish Passage Conditions 2 Evaluation of passage conditions assumes that all designs meet the fish passage design 3 criteria developed for the preparation of the appraisal-level designs (see Section 5.2.6) 4 and fish screening criteria established in NMFS 2008.
5 Upstream passage conditions for adult salmon and downstream passage conditions for 6 juvenile salmonids were evaluated separately. Where upstream-migrating fish encounter 7 artificial structures, passage is via fish ladders, so the total number structures and the total 8 number of steps that a fish must pass was used to evaluate upstream fish passage.
9 Downstream fish passage conditions for juvenile salmonids is evaluated by tallying the 10 number of fish screens that juvenile fish would pass or move through and the number of 11 potential predation sites at structures (including bifurcation structures, ladders, and fish 12 screen outlets). All structures tend to increase predation risk to juveniles because they 13 may provide atypical riverine conditions, create unfavorable localized hydraulic 14 conditions, and create habitat that can be used by predatory fish to feed. Although design 15 measures and management strategies can be used to alleviate some of the predation risk, 16 it may be that predation cannot be fully eliminated.
17 Evaluation Criteria 18 Evaluation criteria associated with fish habitat and passage and the approach to 19 quantifying the criteria are described below.
20 Floodplain Characteristics 21 • Rearing habitat: total acres of floodplain with a depth greater than 1.0 feet at 22 2,500 cfs 23 • Shallow Water Habitat Quality: a rating based on the proportion of very shallow 24 water habitat (less than 0.5 feet) to the amount of rearing habitat (greater than 1.0 25 feet)
26 Passage Conditions for Adult Chinook Salmon 27 • Artificial structures in the migratory path: number of structures that adult salmon 28 would need to pass. Each drop structure, dam sill, fish ladder (or bifurcation 29 structure), and crossing is considered as an individual structure. 30 • Total number of steps at structures: the number of steps an adult salmon would 31 need to jump or swim through. Each drop structure, dam sill, and fish ladder step 32 is considered as an individual step.
33 Passage Conditions for Juvenile Chinook Salmon 34 • Fish screens along the migratory path: the number of fish screens with large 35 diversion rates (greater than 100 cfs) that juvenile salmon may encounter along 36 the migratory path. 37 • Potential predation sites at structures: the number of potential predation sites that 38 juvenile salmon may encounter along the migration path. Each drop structure, 39 dam sill, fish ladder (or bifurcation structure), fish screen system, and crossing is 40 considered a potential predation site.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-9 – October 2012 San Joaquin River Restoration Program
1 Criteria initially identified but not evaluated 2 Several other criteria were initially identified in the Analytical Tools TM (SJRRP 2010f) 3 for evaluating fish habitat and passage in the Project. These addressed the amount of 4 habitat in the main channel, frequency of pools and bars, main channel width, average 5 pool depth, floodplain habitat features, length of banks with bordering riparian 6 vegetation, and floodplain connectivity. These criteria were removed for the reasons 7 described below.
8 • The main channel habitat does not vary significantly between the different 9 Floodplain Initial Alternatives, so this analysis would not produce information 10 with which to compare alternatives and was removed from the evaluation. 11 • No modifications to the main channel are proposed, so the average channel width 12 and depth does not vary amongst alternatives and these criteria were removed 13 from the evaluation. 14 • Two-dimensional (2D) modeling completed in advance of the evaluation was 15 conducted on a limited basis and was not available to evaluate the Initial 16 Alternatives on the basis of in-channel habitat favored by native vs. non-native 17 fishes (pools and bars). While the model results did provide some useful results 18 for velocities on the floodplains, the overall assessment of areas of low to 19 moderate velocities did not provide a tool that discriminated between the 20 alternatives. 21 • In-channel velocities, which vary somewhat dependent on water depth and, 22 therefore, floodplain width, were found to not limit fish passage within the reach, 23 so this criteria was removed from the evaluation. 24 • There was no tool available to evaluate floodplain habitat features that favor 25 native over non-native fishes. These features also do not exist on some of the 26 wider floodplain options, which would occupy land now in agricultural 27 production outside of the existing levees. 28 • Since all banks are proposed to be planted with riparian vegetation, the length of 29 banks with bordering riparian vegetation is a function of channel length only, 30 which does not vary with the Floodplain Initial Alternatives, so this criterion was 31 removed from the evaluation. 32 • While the concept of floodplain connectivity would be of interest, the ability to 33 measure or develop a mechanism to evaluate this was not successful. 34 Connectivity was originally conceptualized as the ratio of total floodplain area to 35 channel length (in acres per foot of channel). This varies by both flow magnitude 36 and floodplain width such that at low flows, very little of the channel may be 37 “connected” while at higher flows, almost all of it is connected. Since this is more 38 a function of the capacity of the channel and has little to do with the floodplain 39 itself, this assessment tool was also removed from the evaluation. 40 • For water temperature during migration, air temperature, wind speed, and 41 vegetative cover were found to have an effect on water temperature. However, 42 water depth on the floodplain, which is a function of width, was found to be far 43 less significant. Since all the Floodplain Initial Alternatives include planting the
Mendota Pool Bypass and Reach 2B Improvements Project 6-10 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 floodplain with woody riparian and floodplain vegetation, and the Project has no 2 effect on air temperature and wind speed, the alternatives were found to not have 3 varying effects on water temperature, so this criterion was removed from the 4 evaluation.
5 6.2.3 Habitat Restoration 6 The discussion below provides background information and documentation of the 7 approach used in evaluating habitat restoration. Restored habitat in the three Bypass 8 Initial Alternatives is evaluated separately from that associated with the Floodplain Initial 9 Alternatives.
10 Vegetation 11 The evaluation assumes the riverbank and areas between the levees would be planted 12 following construction and then irrigated and managed as necessary during the 13 establishment and monitoring periods. This assumption is included in all alternatives in 14 the evaluation in order to compare their restoration potentials. Conceptual planting 15 layouts utilizing native plant wetland and riparian vegetation alliances were developed 16 for each alternative. Individual alliances were distributed along the river based on:
17 • Observations of existing vegetation alliances distribution in relationship to the 18 pre-interim flows 19 • The water demand of dominant species in the vegetation alliance 20 • Wetland status of the dominant species in the vegetation alliance 21 • Potential flooding depth/water surface elevation 22 • Potential flooding duration 23 • Water velocities during high water events 24 • Existing soil types 25 • Levee maintenance requirements
26 Sensitive Vegetation Alliance Extent 27 The future sensitive vegetation alliance3 extent is based on the extent of vegetation 28 communities shown on the Preliminary Planting Plans, and it represents the projected 29 vegetation cover acreage within the floodplain corridor by plant community. The 30 floodplain corridor is the area associated with each of the Initial Alternatives and 31 confined by the levees. The acreages were calculated in GIS.
3 For the purpose of this document, special status vegetation alliances are defined as natural communities that are of limited distribution statewide or within a county or region and are often vulnerable to environmental impacts of projects. These natural communities may or may not contain special status species or their habitat. The current version of the List of California Vegetation Alliances (CDFG 2009) indicates vegetation alliances of high inventory priority as globally or State ranked 1-3 (critically imperiled, imperiled, and vulnerable) for conservation status. Most types of wetlands and riparian communities are considered special status vegetation alliances due to their limited distribution in California. These high- priority vegetation alliances often contain special-status plants.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-11 – October 2012 San Joaquin River Restoration Program
1 Wetlands and Other Waters of the United States Area 2 All vegetation communities proposed in the Preliminary Planting Plans are wetland 3 (hydrophytic) vegetation alliances. It is assumed that Restoration Flows will provide 4 sufficiently frequent inundation of the floodplain to support wetland hydrology. 5 Therefore, the extent of future wetlands is based on the extent of hydric soils in the 6 project area. The area of hydric soils is assumed to be the extent of future jurisdictional 7 wetlands and other waters of the U.S. in the near-term, post-restoration because the other 8 two criteria for a wetland, hydrophytic vegetation and wetland hydrology, will be 9 provided by the Project and the SJRRP. The area of hydric soils was calculated in GIS 10 using the National Resource Conservation Service’s GIS-based soils maps and the lists of 11 hydric soils for Fresno and Madera counties.
12 Wildlife 13 Vegetation restoration has the potential to support various wildlife species native to the 14 area. The following discusses the criteria used to evaluate potential wildlife use.
15 Wildlife Habitat Extent 16 Following construction and revegetation, the Project would provide potential habitat for 17 special-status species. To determine the types of habitat that would be present, a 18 crosswalk (Table 6-2) was created between the sensitive vegetation alliances used in the 19 Preliminary Planting Plans and the existing wildlife habitat types present within the 20 Project area.
21 Table 6-2. 22 Wildlife habitat crosswalk Sensitive Vegetation Alliances Wildlife Habitat Type
California bulrush marsh Fresh emergent wetland Riparian bank forbs and herbs Fresh emergent wetland Buttonbush willow thickets Riparian scrub Black willow thickets Willow scrub Sandbar willow thickets Willow scrub Oregon ash groves Valley foothill riparian Salt grass flats Wet herbaceous California mugwort brush Riparian scrub Fremont cottonwood forest Valley foothill riparian Creeping rye grass turfs Wet herbaceous 23
24 Special Status Species Habitat Extent 25 Existing habitats in the project area have been assessed for suitability for special-status 26 species. This knowledge of wildlife usage in the project area was then used to predict the 27 species’ habitat that would be available following revegetation. Species-specific habitat 28 layers were created based on wildlife habitat types provided by the Preliminary Planting 29 Plans and wildlife usage assumptions outlined in Section 6.3.4. The species-specific
Mendota Pool Bypass and Reach 2B Improvements Project 6-12 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 habitat layers were then used to calculate acres of habitat potentially provided by each 2 Initial Alternative.
3 Evaluation Criteria 4 • Wetlands and other waters of the U.S. area: the acreage of restored habitat with 5 hydrophytic vegetation and on hydric soils. 6 • Sensitive vegetation alliance extent: the acreage of potential future sensitive 7 vegetation alliances based on the Preliminary Planting Plans. 8 • Wildlife habitat extent: the acreage of potential future wildlife habitat types 9 resulting from the restoration. 10 • Special status species habitat extent: the acreage of potential future habitat for 11 special status wildlife species based on the wildlife habitat types. 12
13 Criteria initially identified but not evaluated 14 Other criteria were initially identified in the Analyitical Tools TM (SJRRP 2010f) for 15 evaluating the costs of the Project. These criteria were removed for the reasons described 16 below.
17 • Special status plant species extent was removed from the evaluation because field 18 surveys of listed plants could not be completed prior to the evaluation. 19 • Invasive species establishment potential is not considered to vary significantly 20 amongst the alternatives, so this criterion was removed from the evaluation. 21 • Floodplain vegetation species diversity is a difficult metric to predict at this stage 22 of the Project. All the Initial Alternatives propose ten sensitive vegetation 23 alliances to restore vegetation on the floodplain. While greater species diversity 24 within those alliances may rely on larger patches to support listed plants, design 25 details and modeling during the appraisal level design are not capable of 26 predicting how diverse vegetation alliances may be. Additionally, the amount, 27 extent, and location of diversity is difficult to quantify. Based on these reasons, 28 this criterion was removed from the evaluation. 29 • Total shaded riverine aquatic habitat area: There are no changes proposed to the 30 river channel, and all Initial Alternatives include similar planting strategies, 31 resulting the same areas of shaded riverine habitat in all Initial Alternatives; 32 therefore, this criterion was removed from the evaluation.
33 6.2.4 Geomorphology 34 The discussion below provides background information and documentation of the 35 approach used in evaluating channel geomorphology. Geomorphology in the three 36 Bypass Initial Alternatives is evaluated separately from that associated with the 37 Floodplain Initial Alternatives.
38 Analyses of channel vertical stability, lateral migration potential, and overall channel 39 stability were completed using 2008 LiDAR data, bed-material transport capacity rating 40 curves, hydraulics from HEC-RAS, flow records from the SJRRP CalSim model, bed
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-13 – October 2012 San Joaquin River Restoration Program
1 material gradations, historical aerial photographs, previous levee and bank erosion risk 2 studies, bedload transport modeling, and bank energy indices (Tetra Tech 2011b). As 3 described below, neither the analyses of channel vertical stability nor overall channel 4 stability showed that these criteria would be differentiators for the alternatives and were, 5 therefore, eliminated.
6 Lateral Migration Potential 7 The analysis of the lateral migration potential reviewed previous levee and bank erosion 8 risk studies and updated those analyses with the Restoration Flows to calculate the bank 9 energy index associated with the Initial Alternatives. Based on the bank energy index, 10 the existing vegetative cover, and the proximity of the channel to the proposed levee, the 11 erosion hazard potential of the various channel banks was qualitatively assessed. Typical 12 erosion protection concepts and costs were developed and weighted based on the 13 qualitative hazard potential. The weighted costs for each bank section were summed to 14 obtain the total estimated erosion protection cost for each Initial Alternative.
15 Evaluation Criteria 16 Evaluation criteria associated with geomorphology and the approach to quantifying the 17 criteria are described below.
18 • Potential for lateral migration to impact levees: The estimated cost of providing 19 erosion protection (revetment) on levees that may be impacted by lateral erosion.
20 Criteria initially identified but not evaluated 21 Other criteria were initially identified in the Analyitical Tools TM (SJRRP 2010f) for 22 evaluating the costs of the Project. These criteria were removed for the reasons described 23 below.
24 • Channel vertical stability: The analysis showed no significant differences in 25 vertical channel stability (channel degradation or aggradation) are anticipated 26 among the various Floodplain and Bypass Initial Alternatives, so this criterion 27 was eliminated from the evaluation. 28 • Potential to reach a future stable channel configuration in dynamic equilibrium: 29 This analysis is expected to show no significant differences in future stable 30 channel cross-section or equilibrium slope for the various Floodplain and Bypass 31 Initial Alternatives, so this criterion was eliminated from the evaluation.
32 6.3 Preliminary Impact Assessment
33 The sections below describe the criteria chosen to represent the range of impacts 34 associated with the Initial Alternatives.
35 6.3.1 Groundwater 36 The discussion below provides background information and documentation of the 37 approach used in evaluating seepage impacts. Seepage impacts in the three Bypass Initial
Mendota Pool Bypass and Reach 2B Improvements Project 6-14 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 Alternatives are evaluated separately from that associated with the Floodplain Initial 2 Alternatives.
3 Seepage Impacts 4 Cross-sectional seepage modeling developed in MODFLOW-SURFACT was used to 5 estimate the potential for water levels to exceed the monitoring threshold at distances 6 within one mile of the river. Output from the cross-sectional seepage modeling was 7 exported to GIS and used to delineate the approximate areas where monitoring thresholds 8 may be exceeded. Acreages of shallow groundwater were also estimated. The analysis is 9 intended to provide a relative comparison between Initial Alternatives; it is not intended 10 or capable of being compared to baseline conditions.
11 Evaluation Criteria 12 • Acres of land in which groundwater levels rise above 5-foot monitoring threshold: 13 The acreage of land outside the proposed levee alignments that is anticipated to 14 have shallow groundwater elevations above the 5-foot monitoring threshold and is 15 thus subject to mitigation measures to prevent waterlogging. 16 • Acres of land in which groundwater levels rise above 7-foot monitoring threshold: 17 The acreage of land outside the proposed levee alignments that is anticipated to 18 have shallow groundwater elevations above the 7-foot monitoring threshold and is 19 thus subject to mitigation measures to prevent waterlogging.
20 6.3.2 Land Use 21 The discussion below provides background information and documentation of the 22 approach used in evaluating land use impacts. Land use impacts in the three Bypass 23 Initial Alternatives is evaluated separately from that associated with the Floodplain Initial 24 Alternatives.
25 Crop Acreage 26 Land use impacts focus exclusively on agricultural uses in the project area. Agricultural 27 impacts are based on the amount of active cropland that would be taken out of production 28 under the Initial Alternatives and crop data from field surveys and communications with 29 landowners. Only alfalfa, almond, grapes, other row crops (grouped), palm, and 30 pistachio production were considered.
31 Evaluation Criteria 32 • Acres of farmland removed from production: The total acres of alfalfa, almond, 33 grapes, other row crops (grouped), palm, and pistachio that would be removed 34 from production due to the construction of the Initial Alternatives.
35 6.3.3 Socioeconomics and Economics 36 The discussion below provides background information and documentation of the 37 approach used in evaluating socioeconomics and economics impacts. Socioeconomics 38 and economics impacts in the three Bypass Initial Alternatives are evaluated separately 39 from that associated with the Floodplain Initial Alternatives.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-15 – October 2012 San Joaquin River Restoration Program
1 Agricultural Economic Impacts 2 Agricultural economic impacts are based on the annual value of crop production that 3 would be lost with taking land out of production (in acres) multiplied by representative 4 crop production values ($/acre). Representative crop production values are based on 5 historical estimates as presented in county agricultural commissioner reports for Fresno 6 and Madera counties. Historical data between 2004 and 2008 were evaluated. Historical 7 data were first adjusted to 2010 dollars using the consumer price index and then 8 normalized to develop average annual values per acre for different types of crops grown 9 in the project area. Representative per-acre production values used in the analysis are:
10 • Almonds (Fresno County): $5,020/acre 11 • Almond (Madera County): $4,121/acre 12 • Grapes (Fresno County): $3,975/acre (using a weighted average for raisin, table, 13 and wine grape production values) 14 • Pistachio (Fresno County): $6,037/acre 15 • Palm (Fresno and Madera Counties): $52,769/acre (using miscellaneous nursery 16 crop production for all counties that report acres and values in the agricultural 17 commissioner reports) 18 • Grazing (Fresno County): $8.74/acre 19 • Vacant land (Fresno County): $8.74/acre (assumed to be comparable to grazing 20 land values) 21 • Vacant land (Madera County): $12.88/acre (assumed to be comparable to grazing 22 land values) 23 • Non-Agricultural (Fresno and Madera Counties): $0/acre (it is assumed that no 24 agricultural production occurs on these lands) 25 The regional economic impacts (i.e., output, employment, and income) associated with 26 changes in agricultural production have not been quantified as part of the alternatives 27 evaluation; this analysis will occur as part of the EIS/R process using regional economic 28 models. Based on declines in crop production values, there would be an ancillary decline 29 in regional economic activity and associated benefits in the project area.
30 The regional economic impacts (i.e., output, employment, and income) associated with 31 construction and operations, maintenance, and repair activities have not been quantified 32 as part of the alternatives evaluation; this analysis will occur as part of the EIS/R process. 33 Based on anticipated expenditures in the project area, there would be an ancillary 34 increase in regional economic activity and benefits in the project area.
35 The fiscal impacts of the project on local municipalities have not been quantified as part 36 of the alternatives evaluation; this evaluation will occur as part of the EIS/R process.
37 The financial impacts to local landowners have not been quantified as part of the 38 alternatives evaluation; this evaluation will occur as part of the EIS/R process. It is 39 anticipated that landowner impacts will be negligible assuming that they are compensated 40 at fair market value for their properties.
Mendota Pool Bypass and Reach 2B Improvements Project 6-16 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 Evaluation Criteria 2 • Reduction in annual agricultural production values: The total production value 3 based on unit production values and the acreage removed from production due to 4 the construction of the Initial Alternatives.
5 6.3.4 Environmental 6 The discussion below provides background information and documentation of the 7 approach used in the preliminary environmental impacts evaluation. Environmental 8 impacts in the three Bypass Initial Alternatives are evaluated separately from that 9 associated with the Floodplain Initial Alternatives.
10 Special Status Vegetation
11 Wetlands 12 Data on field delineated wetlands was not available for the alternatives evaluation. The 13 National Wetlands Inventory maps were used as a basis for calculating impacts to 14 wetlands in the project area.
15 To calculate the direct impact of Project activities, including grading, levee construction, 16 and the placement of fill, a direct impact layer was created for each Initial Alternative to 17 map all areas where direct impacts are anticipated. Each Initial Alternative’s impact layer 18 was overlain with the National Wetlands Inventory layer to calculate the area of direct 19 impact to potential wetlands, represented by the intersection of the two layers. Direct 20 impacts to potential wetlands will result in the loss of that habitat.
21 Sensitive Vegetation Alliances 22 The Environmental Field Survey TM (SJRRP 2010b) documents the mapped sensitive 23 vegetation alliances occurring with the project area. These mapped alliances were used 24 to calculate direct impacts to sensitive vegetation alliances from the Initial Alternatives.
25 To calculate the direct impact of Project activities, including grading, levee construction, 26 and the placement of fill, a direct impact layer was created for each Initial Alternative to 27 map all areas where direct impacts are anticipated. Each Initial Alternative’s impact layer 28 was overlain with the sensitive vegetation alliances layer to calculate the area of direct 29 impact to sensitive vegetation alliances, represented by the intersection of the two layers. 30 Direct impacts to sensitive vegetation alliances will result in the loss of that habitat.
31 Special Status Wildlife 32 The Environmental Field Survey TM (SJRRP 2010b) provides an assessment of the State 33 or Federally listed wildlife species that are likely to occur in the Project area and are, 34 therefore, likely to be impacted by the Project. Based on the information presented in the 35 Environmental Field Survey TM, the following nine listed wildlife species were selected 36 for inclusion in this alternatives analysis:
37 • Blunt-nosed leopard lizard (Gambelia sila), Federally and State listed as 38 endangered, and CDFG Fully Protected
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-17 – October 2012 San Joaquin River Restoration Program
1 • Fresno kangaroo rat (Dipodomys nitratoides exilis), Federally and State listed as 2 endangered 3 • Giant garter snake (Thamnophis gigas), Federally and State listed as threatened 4 • Greater sandhill crane (Grus canadensis tabida), State listed as threatened, CDFG 5 Fully Protected, and protected under the Migratory Bird Treaty Act 6 • Longhorn fairy shrimp (Branchinecta longiantenna), Federally listed as 7 endangered 8 • San Joaquin kit fox (Vulpes macrotis mutica), Federally and State listed as 9 endangered 10 • Swainson's hawk (Buteo swainsoni), State listed as threatened and protected under 11 the Migratory Bird Treaty Act 12 • Valley elderberry longhorn beetle (Desmocerus californicus dimorphus), 13 Federally listed as threatened 14 • Vernal pool fairy shrimp (Branchinecta lynchi), Federally listed as threatened 15 To quantify impacts to these species and allow for comparison between alternatives, 16 impacts are defined in terms of acres4 of potential habitat lost or altered for each species. 17 The following sections describe how potential habitat was defined and how impacts were 18 calculated.
19 Species Habitat Layers 20 Habitat layers were created for each species to estimate the location and area of potential 21 habitat present within the Project area under existing conditions. Each species-specific 22 habitat layer is based on the wildlife habitat types layer5, which identifies the wildlife 23 habitat types present in the project area. The wildlife habitat types layer is a product of 24 the wildlife habitat assessment and habitat mapping effort described in the Environmental 25 Field Survey TM (SJRRP 2010b). The wildlife habitat types layer was adapted to create 26 species-specific layers according to the rules outlined below. These rules are based on 27 assumptions developed from available data about species’ use of specific wildlife habitat 28 types.
29 • Blunt-nosed Leopard Lizard: Suitable upland habitat types, including annual 30 grassland and elderberry savannah, within the southeastern portion of the study 31 area are designated as habitat for the blunt-nosed leopard lizard. 32 • Fairy Shrimp: Longhorn fairy shrimp and vernal pool fairy shrimp have similar 33 habitat requirements; therefore, a single habitat layer was created to estimate 34 potential impacts to both species and they are addressed collectively as “fairy 35 shrimp”. Because access allowing a more informed assessment has not been
4 Impacts to listed wildlife are discussed in terms of acres except for the valley elderberry longhorn beetle for which impacts are typically discussed in terms of the number of individual elderberry shrubs lost. Both the acreage and the number of shrubs are provided the summary tables in Section 7.0. 5 The valley elderberry longhorn beetle is an exception because the habitat layer for this species was created using a combination of point data and vegetation mapping of elderberry stands.
Mendota Pool Bypass and Reach 2B Improvements Project 6-18 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 available, all potential seasonal wetland is designated as habitat for these species. 2 Per USFWS guidance (USFWS 1996), any direct impact within 250 feet of a 3 discrete unit of potential seasonal wetland habitat was considered to impact the 4 entire unit. Additionally, any direct impact to a discrete unit of potential seasonal 5 wetland was considered to directly impact the entire unit. 6 • Fresno Kangaroo Rat: For Fresno kangaroo rat, habitat was defined as annual 7 grassland and elderberry savannah within the southeast portion of the study area. 8 • Giant Garter Snake: Habitat for the giant garter snake includes the following 9 habitat categories, aquatic, upland and wetland. Aquatic habitat is defined as all 10 lacustrine habitat within the Project area, which has been present during the 11 snake’s active period in the San Joaquin River west of the San Mateo Road 12 crossing (the Mendota Pool). Per USFWS guidance (USFWS 2005), suitable 13 upland habitat within 200 feet of the lacustrine habitat was designated as upland 14 habitat for this species, including the following habitat types: annual grassland, 15 barren, riparian scrub, river wash, valley foothill riparian, wet herbaceous, and 16 willow scrub. All fresh emergent wetland within the 200-foot buffer is defined as 17 wetland habitat for this species. 18 • Greater Sandhill Crane: Winter foraging habitat for the greater sandhill crane is 19 defined as all annual grassland, fresh emergent wetland, irrigated hayfield, 20 cropland, irrigated row and field crop, pasture, and wet herbaceous habitat within 21 the project area. 22 • San Joaquin Kit Fox: Habitat for the San Joaquin kit fox is defined as all annual 23 grassland, elderberry savannah, barren, and pasture habitat within the project area. 24 • Swainson's Hawk: Swainson’s hawk habitat includes two categories, foraging and 25 nesting. Foraging habitat is defined as all annual grassland, barren, elderberry 26 savannah, irrigated hayfield, wet herbaceous, and pasture habitat within the 27 project area. All valley foothill riparian habitat is considered nesting habitat. 28 Additionally, nesting habitat is expanded to include up to approximately 0.5 acres 29 centered on observed nesting sites as recorded in the California Natural Diversity 30 Database (CDFG 2010), regardless of the wildlife habitat type designation 31 assigned to the vegetation at that location. 32 • Valley Elderberry Longhorn Beetle: Habitat for valley elderberry longhorn beetle 33 is quantified in terms of elderberry shrubs (Sambucus spp.); therefore, the habitat 34 layer for this species was created through a different process than that of other 35 species evaluated. To create a habitat layer for valley elderberry longhorn beetle, 36 point data mapping the location of known elderberry shrubs created in 2002 37 (ESRP 2006) was combined with elderberry stands mapped in 2010 during 38 special-status vegetation alliance surveys completed for the Project. All points 39 that overlapped with mapped elderberry stands were excluded to avoid double 40 counting. Impacts are typically discussed in terms of individual shrubs, so the 41 approximate number of shrubs was calculated by estimating the density of shrubs 42 and multiplying by the acreage. For the purposes of this analysis only, the density 43 of elderberry shrubs within the Project area was estimated to be 42 shrubs per acre 44 in the riparian zone and 9 shrubs per acre in areas of elderberry savannah. Impacts
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-19 – October 2012 San Joaquin River Restoration Program
1 were also quantified in terms of acres for the evaluation in order to sum all habitat 2 impacts.
3 Impact Calculations 4 The anticipated impacts of the Project alternatives were calculated in GIS using the 5 species habitat layers described above.
6 To calculate the direct impact of Project activities, including grading, levee construction, 7 and the placement of fill, a direct impact layer was created for each alternative to map all 8 areas where direct impacts are anticipated. Each alternative’s impact layer was overlain 9 with each species habitat layer to calculate the area of direct impact to potential habitat, 10 represented by the intersection of the two layers. Direct impacts to potential species 11 habitat will result in the loss of that habitat and, therefore, a potential direct impact to 12 listed wildlife species.
13 In addition to direct impacts that occur at the time of construction, the Project may also 14 result in indirect impacts to listed wildlife species as a result of habitat change that occurs 15 over time due to changes in hydrology. New hydrologic patterns may alter the existing 16 vegetation present within the Project area which may cause new habitat types to 17 gradually replace existing habitats, and existing farmland within the project area will be 18 planted with native riparian and floodplain habitats appropriate for the new hydrologic 19 regime. All habitat areas anticipated to be altered due to changes in hydrology are 20 considered to be indirectly impacted. Although indirect impacts are anticipated for the 21 Project, the acreage of indirect impacts was not calculated for the alternatives evaluation.
22 Cultural and Historical Resources 23 The following sections describe the assessment of the potential for cultural and historic 24 resources to be impacted by the Initial Alternatives. Limited surface investigations for 25 cultural and historic resources have been completed based on access availability; 26 however, some areas could not be investigated due to access restrictions, and no 27 subsurface investigations have been completed.
28 Historic properties 29 Record searches were conducted through the South San Joaquin Valley Information 30 Center (SSJVIC). The information center staff accessed the records for the Mendota, 31 Firebaugh, and Tranquility (USGS) 7.5-minute quadrangles, including a one-mile radius 32 around the project extent. The following references were also reviewed:
33 • NRHP National Register of Historic Places 34 • California Register of Historical Resources 35 • Office for Historic Preservation Historic Property Directory 36 • California State Historical Landmarks listing 37 • California Inventory of Historic Resources 38 • California Points of Historical Interest listing 39 • The Caltrans State and Local Bridge Survey
Mendota Pool Bypass and Reach 2B Improvements Project 6-20 – October 2012 Attachment A – Initial Alternatives Evaluation 6.0 Initial Alternatives Evaluation Criteria
1 • Historical maps, including GLO Plat Maps 2 The number of previously recorded sites was used to evaluate alternatives. No previously 3 recorded National Register or California Register eligible resources were identified in the 4 records search.
5 Buried deposits sensitivity 6 Landform age classes can be associated with a qualitative sensitivity for buried deposits 7 (Byrd 2009). Each sensitivity class was assigned a numerical rating for the purposes of 8 the alternatives evaluation (see Table 6-3). Landform age classes mapped by Fresno and 9 Madera counties were overlain with the extents of the Initial Alternatives, and the highest 10 sensitivity class within the extent of each Initial Alternative was noted.
11 Table 6-3. 12 Buried deposits sensitivity according to landform age class Map Sensitivity Class Landform Symbol Rating Historical to Modern Fans, Floodplains, Artificial Fill, Low to High and Cuts; Water Hm 51 Pre Pleistocene through Latest Pleistocene Hillslopes, Very Low Fans, and Floodplains pP, pQ, OP 1 Low Early Holocene Fans and Floodplains LtP, EH 2 Moderate Middle Holocene Fans and Floodplains MH 3 High Late Holocene Fans and Floodplains LH 4 Very High Latest Holocene Fans and Floodplains LtH 5 13 Based on Byrd 2009. 14 1 Assumed high sensitivity to be conservative. 15
16 Evaluation Criteria 17 • Wetland impacts: The estimated acreage of direct impacts to wetlands resulting 18 from the Initial Alternatives. 19 • Sensitive vegetation alliance direct impacts: The estimated acreage of direct 20 impacts to sensitive vegetation alliances resulting from the Initial Alternatives. 21 • Special status wildlife habitat impacts: The estimated acreage of direct impacts to 22 special status wildlife habitat resulting from the Initial Alternatives. 23 • Historic properties potentially effected: The number of recorded historic 24 properties identified within the extents of the Initial Alternatives. 25 • Buried deposits sensitivity: The highest buried deposits sensitivity within the 26 extents of the Initial Alternatives based on the landform age scale.
27 6.4 Scoring Alternatives Data and Professional Judgment
28 Most of the data presented use objective measurements for each criterion, such as acres, 29 dollars, or miles, based on appraisal-level designs for each alternative. Some of the
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 6-21 – October 2012 San Joaquin River Restoration Program
1 criteria in the evaluation use qualitative assessments and rely on professional judgment to 2 estimate results. Assumptions about current conditions and future effects of the 3 alternatives are inherently involved at the current level of design. These assumptions 4 have been based on information collected from similar projects and professional 5 experience.
6
Mendota Pool Bypass and Reach 2B Improvements Project 6-22 – October 2012 Attachment A – Initial Alternatives Evaluation
1 7.0 Initial Alternatives Descriptions 2 This chapter describes the Initial Alternatives developed for the Project. Initial 3 Alternatives are presented for each the floodplain and bypass components individually. 4 Following the alternatives evaluation, an Initial Alternative for each component will be 5 combined together to form the Final Alternatives, which are complete Project alternatives 6 that will be evaluated in the Project EIS/R. For example, a Floodplain Initial Alternative 7 will be combined with a Bypass Initial Alternative to form a Final Alternative. Factors 8 that will influence the selection of Initial Alternatives include whether they comply with 9 the terms of the Settlement, whether they substantially meet the Project goals and 10 objectives, and whether their benefits are seen to offset their impacts. Final Alternatives 11 will then be assessed for environmental impacts to the various resource areas in the 12 Project EIS/R.
13 7.1 Floodplain Initial Alternatives
14 The Floodplain Initial Alternatives include:
15 • Building levees capable of conveying flows up to 4,500 cfs 16 • Restoring floodplain habitat to provide benefit to salmonids and other native 17 fishes 18 in the portion of Reach 2B between the Chowchilla Bifurcation Structure (approximately 19 RM 216) and the head of the Settlement Alignment Bypass Initial Alternative 20 (approximately RM 207.7). (Additional floodplain area downstream of the head of the 21 Settlement Alignment Bypass Initial Alternative associated with the Compact Alignment 22 Bypass Initial Alternative and the Fresno Slough Dam Initial Alternative is considered 23 part of those Initial Alternatives and is discussed is Sections 7.2.3 and 7.2.4, 24 respectively). See Figure 7-1.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-1 – October 2012 San Joaquin River Restoration Program
1
2 Figure 7-1. 3 Levee Alignments for Floodplain Initial Alternatives
4 The purpose of the floodplain is to provide riparian and floodplain habitat and support the 5 migration and transient rearing of salmonids and other native fishes in Reach 2B. Five 6 alternative levee alignments (FP-1 through FP-5) with varying widths and varying 7 amounts of floodplain grading will increase the habitat and capacity in Reach 2B. 8 Elements of the designs include:
9 • Fish habitat and passage 10 • Floodplain and riparian habitat restoration 11 • Construction of new levees 12 • Removal or partial removal of existing levees 13 • Floodplain grading 14 • Retrofit the San Joaquin control structure at the Chowchilla Bifurcation Structure 15 with a fish ladder 16 • Existing infrastructure relocations or floodproofing 17 • Replacement of San Mateo Avenue crossing 18 • Levee protection 19 • Lone Willow Slough fish screen 20 • Land acquisition
Mendota Pool Bypass and Reach 2B Improvements Project 7-2 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 7.1.1 Elements Common to All Floodplain Initial Alternatives 2 The following sections describe the elements that are common to all Floodplain Initial 3 Alternatives.
4 Fish Habitat and Passage 5 One of the primary focuses of the Floodplain Initial Alternatives is to provide floodplain 6 and riparian habitat in support of migrating juvenile and adult salmonids and other native 7 fishes. Floodplain and riparian habitats included in the Floodplain Initial Alternatives are 8 a variety of native plant communities suited to the hydrology, soils, and climate of Reach 9 2B and the San Joaquin Valley (see additional discussion below under Habitat 10 Restoration). Vegetation communities that provide the greatest benefits for juvenile 11 salmonids (annual grassland communities; Jeffres 2008) were preferred wherever those 12 communities were also supported by the hydrology of the Restoration Flows. Based on 13 the floodplain modeling, inundation depths less than 1.0 foot represent 28-53% of total 14 floodplain area, and depths less than 0.5 feet represent 12-25% of total floodplain area, 15 depending on the Floodplain Initial Alternative.
16 The Floodplain Initial Alternatives also include provision of fish passage through 17 structures for salmonids and other native fish. These structures include a culverted 18 crossing at San Mateo Avenue, fish screens, fish passage facilities, grade control 19 structures, bifurcation structures (under certain flows), and Mendota Dam. The designs 20 for structures with fish passage components would be based on criteria in Anadromous 21 Salmonid Passage Facility Design (NMFS 2008) and Guidelines for Salmonid Passage 22 at Stream Crossings (NMFS 2001). Specifically, the alternatives will provide suitable 23 hydraulic conditions for passage of up-migrating adult and juvenile salmonids, out- 24 migrating juvenile salmonids, and inter-reach migration of other native fish between 25 Reach 2A and Reach 3. Suitable hydraulic conditions include those conditions which the 26 species is physically capable of passing and do not cause undue stress on the animal. The 27 passage features are designed to cause no physical harm. See Fish Passage Design 28 Criteria in Section 5.2.6.
29 The Floodplain Initial Alternatives include three facilities that fish would encounter or 30 need to pass to migrate between Bypass Initial Alternatives and Reach 2A (from 31 downstream to upstream): San Mateo Avenue crossing, Lone Willow Slough fish screen, 32 and the Chowchilla Bifurcation Structure with fish ladder. Each structure represents a 33 potential stressor for adult salmon and potential predation site for juvenile salmon. 34 However, each structure is designed to perform according to the fish passage design 35 criteria. In addition, the channel and floodplain incorporate riparian plantings to provide 36 cover, woody material, and velocity variability, while the design footprint allows 37 sufficient space to accommodate channel structure variability. All of which may help to 38 reduce stress and predation.
39 Habitat Restoration 40 For the evaluation, it is assumed that active riparian and floodplain habitat restoration 41 would occur in the Floodplain and Bypass Initial Alternatives. It is assumed that native 42 plant wetland vegetation alliances consisting primarily of obligate, facultative-wet, and 43 facultative species, similar to species historically present, will thrive within the main
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-3 – October 2012 San Joaquin River Restoration Program
1 channel. Eventually, a mosaic of riparian habitat types will develop along the main river 2 channel banks consisting of cottonwood forests, willow scrublands, riparian wetlands, 3 herbaceous meadows with sedges, rushes and grasses, and occasional groves of Oregon 4 ash (Figure 7-2).
5
6 Figure 7-2. 7 Typical distribution of vegetation alliances along a Reach 2B riparian bank section
8 Vegetation Alliance Descriptions and Assumptions for their Location 9 Native vegetation alliances that were observed and described during plant community 10 mapping surveys performed for the Environmental Field Surveys TM (SJRRP 2010b) are 11 anticipated to be included in a restoration design.
12 The following vegetation alliances are likely candidates for the ecological restoration of 13 the San Joaquin River channel. They are listed in order of their distance from the ordinary 14 high water mark (OHWM); alliances requiring location near the OHWM are listed first, 15 alliances preferring locations higher up on the floodplain are listed later.
16 • California Bulrush Marsh 17 • Riparian Bank Herbs 18 • Button Willow Thickets (Cephalanthus occidentalis alliance) 19 • Black willow thickets (Salix gooddingii alliance) 20 • Oregon ash groves (Fraxinus latifolia forest alliance) 21 • Saltgrass Flats (Distichlis spicata grassland alliance) 22 • California Mugwort Brush
Mendota Pool Bypass and Reach 2B Improvements Project 7-4 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 • Creeping Wildrye Grassland (Leymus triticoides herbaceous alliance) 2 • Fremont cottonwood forest (Populus fremontii alliance) 3 • Other Vegetation Alliances
4 Maintenance & Invasive Species Control 5 Invasive, non-native species would be removed from the project area during the 6 installation, plant establishment and maintenance periods. Long-term management of the 7 project would consist of removal of the most invasive non-native species within the reach 8 such as giant reed grass (Arundo donax), perennial pepperweed (Lepidium latifolium) and 9 poison hemlock (Conium maculatum). Long-term management would also include 10 removal of other invasive species that are currently found in upstream reaches and may 11 eventually colonize in the project area such as red sesbania (Sesbania punicea), salt cedar 12 (Tamarix species), and Chinese tallow (Sapium sebiferum). Invasives removal 13 techniques may include mechanical removal, root excavation, hand pulling, mowing, 14 disking, controlled burning, grazing, aquatic-safe herbicides, or a combination of 15 techniques as appropriate.
16 While it is not anticipated that major management actions will be needed, the key 17 objective of long-term management would be to monitor and identify any environmental 18 issues that arise, and use adaptive management to determine what actions would be most 19 appropriate to correct these issues.
20 The general management approach to the long-term maintenance of the floodplain areas 21 will be to maintain quality habitat for each natural resource, on-going monitoring and 22 maintenance of key environmental characteristics of the entire floodplain area within the 23 reach. An adaptive management approach will be used to incorporate changes to 24 management practices, including corrective actions as determined to be appropriate by 25 the Bureau of Reclamation. Adaptive management includes those activities necessary to 26 address the effects of climate change, fire, flood, or other natural events, force majeure, 27 etc.
28 The expected long-term management needs and activities necessary to maintain any on- 29 site mitigation sites would be: resource specific long-term maintenance activities and 30 other general maintenance activities such as exotic species elimination, grazing 31 management, clean-up and trash removal, infrastructure management such as gate, fence, 32 road, culvert, signage and drainage-feature repair, and other maintenance activities 33 necessary to maintain the riparian floodplain habitat quality.
34 Temporary Irrigation System and Water Supply 35 Since all of the anticipated plantings are wetland species or borderline wetland species, 36 they would need regular overhead irrigation (typically April through October) during 37 their establishment period (three to five years depending on rainfall conditions and the 38 plants growth rates and vigor). The amount of water needed is estimated to be 39 approximately 2.4 feet per acre per year. They will be irrigated with an extensive 40 temporary surface mounted irrigation system that would provide water for the plants 41 several times a week during the hot months of the year. The irrigation distribution piping
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-5 – October 2012 San Joaquin River Restoration Program
1 would be installed aboveground and anchored to the ground with rebar soil staples so that 2 it would not damaged during high flows that would be regularly inundating the 3 floodplain. The sprinkler heads will be installed on four-foot high, braced standpipes so 4 that their irrigation stream is not blocked or diverted by growing vegetation. The 5 irrigation system will be disassembled and removed at the end of the establishment 6 period.
7 The irrigation water supply could include groundwater wells or water pumped from the 8 river with portable, skid mounted, diesel- or gas-powered pumps and stored in tanks. 9 Additionally, purchases from willing sellers may be required to withdrawal water from 10 the river or other nearby water sources (e.g., Mendota Pool).
11 Existing Native Vegetation Protection 12 The existing native vegetation in the project area designated to remain will be 13 temporarily fenced with orange snow fencing (or equivalent) to prevent entry, driving, 14 parking, or storing equipment or material within these areas during construction. Existing 15 vegetation would be left in place or only minimally trimmed to facilitate access and work 16 at the site. The existing soil is an ideal growing medium for all the desired native plants. 17 In order to maximize plant growth and planting success, existing soil and topsoil would 18 be preserved and disturbance during construction will be minimized to the maximum 19 practicable extent.
20 Maintenance and Monitoring 21 The key maintenance and monitoring activities include close monitoring of installed 22 plants for drought stress and overwatering, removal of competitive, invasive, non-native 23 species, replacement of diseased and dead plants, irrigation system maintenance, and 24 removal of trash and debris.
25 Wildlife 26 As associates of the anticipated vegetation alliances, wildlife habitats and wildlands will 27 develop. The Floodplain Initial Alternatives would provide potential habitat for greater 28 sandhill crane and Swainson’s hawk. The larger floodplains provide increasingly more 29 potential habitat.
30 Levees 31 New levees (FP-1 through FP-5) would be constructed to create varying corridor widths, 32 ranging from just outside of the existing levee alignment, to a corridor width of 33 approximately 5,600 feet (Figure 7-1). The levee alignments for FP-2 and FP-3 are the 34 same; however, FP-3 includes floodplain grading (see discussion in Section 7.1.4).
35 While the length, height, and footprint of the levees vary, the capacity, freeboard, and 36 cross-section are common to all the Floodplain Initial Alternatives. Levees will be 37 designed to maintain 3 feet of freeboard on the levees at 4,500 cfs. Levee design is based 38 on the Corps of Engineers and USACE Engineer Manual 1110-2-1913-Design and 39 Construction of Levees guidelines (USACE 2000) and includes slurry walls to reduce 40 seepage, inspection trenches, maintenances roads, and drainage trenches to direct off-site 41 drainage.
Mendota Pool Bypass and Reach 2B Improvements Project 7-6 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Levee alignments maintain a 300-foot buffer zone, where appropriate, between the levee 2 and river channel to avoid impact to levees over time due to potential channel migration. 3 In areas where a minimum 300-foot buffer zone between the main river channel and 4 levee cannot be maintained, bank revetment is incorporated in the design in accordance 5 with DWR Division of Engineering (DOE) guidelines.
6 The levees would be designed to have sideslopes of 3 horizontal to 1 vertical (3H to 1V) 7 on the waterside and landside. A maintenance road and surface drainage ditch would also 8 be included. Surface drainage ditches would only be intended to capture and direct 9 runoff; they are not intended to address nuisance seepage. Due to historical seepage and 10 lack of geotechnical data, it was assumed for cost purposes that all of both new levees 11 adjacent to potentially impacted lands (approximately 90 percent of the total levee length) 12 would contain slurry walls. By following the USACE standards, all levees without a 13 slurry wall will have an inspection trench. Levees that include a slurry wall would also 14 have an inspection trench. Additional data collection and analysis will be required to 15 verify the groundwater conductivity rates of the in situ and borrow soils and to finalize 16 the seepage control measures.
17 The levee costs are based on the assumptions that suitable earthen fill materials will be 18 available within 1 mile of the levee locations and that some modification to soils may be 19 required to meet permeability requirements. Once the borrow source for the levees is 20 identified, import and hauling costs may be updated.
21 Removal of existing levees 22 All Floodplain Initial Alternatives include removal of portions of the existing levees. 23 Levee removal is designed to expand the inundation area of the floodplain out to the 24 proposed levees and improve connectivity between the river channel and proposed 25 floodplain. The locations of existing levee removal are based upon the hydraulic 26 performance of the channel and floodplain. In certain locations, however, highly 27 desirable existing vegetation (native and sensitive vegetation communities that can serve 28 as seed banks for future vegetation communities) can be found on the existing levees. 29 Where hydraulic performance and connectivity of the floodplain would not be negatively 30 affected, portions of the existing levees with highly desirable vegetation would remain in 31 place.
32 Existing infrastructure relocations or floodproofing 33 Existing infrastructure such as groundwater wells, pumps, electrical and gas distribution 34 lines, water pipelines, and canals are located in the Project area and will require 35 relocation or floodproofing to protect them from future Restoration Flows and increased 36 floodplain area in the Reach 2B corridor. The quantity and extent of relocations varies 37 with each Floodplain Initial Alternative. The cost to perform the relocations and 38 floodproofing is included in the Project cost; the actual relocation or floodproofing work 39 may be performed by others.
40 Electrical and Gas Distribution 41 The length of electrical distribution line impacted by each Floodplain Initial Alternative 42 was identified for possible relocation. Information from PG&E was available for portions
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-7 – October 2012 San Joaquin River Restoration Program
1 of the area in shapefile format and was supplemented by field data. At the current level of 2 design, it was assumed that the same length of electrical and gas distribution line will 3 need to be replaced.
4 Canals and Drains 5 The length of canals impacted by each Floodplain Initial Alternative was identified for 6 possible relocation. On-farm canals and drains visible on the LiDAR imagery (Central 7 Valley Floodplain Evaluation and Delineation (CVFED) 2009) and identified during on- 8 site field meetings with landowners were quantified. At the current level of design, it is 9 unknown how canals and drains outside the project area will be reworked as a result of 10 the impacted canals and drains. To account for the costs of reworking canals and drains, 11 it was assumed that the same length of canals and drains impacted will need to be 12 replaced. A typical canal cross-section and 2007 unit costs were used to estimate the 13 costs of relocation. No subsurface drains were able to be quantified; however, some are 14 believed to exist within the area.
15 Lift Pumps 16 The number of lift pumps impacted by each Floodplain Initial Alternative was identified 17 for possible relocation. Lift pumps visible on the LiDAR imagery (CVFED 2009) or 18 noted in the Calfish database (Pacific States Marine Fisheries Commission 2007) were 19 assumed to require relocation to new facilities on the edge of the proposed levees. A 20 pilot channel dug from the low flow river channel to the intake of the relocated pumps 21 was also assumed. Locations in the Calfish database were confirmed using the LiDAR 22 imagery when possible.
23 Groundwater Wells 24 The number of wells impacted by each Floodplain Initial Alternative was identified for 25 possible floodproofing or relocations. Wells were identified within the area using aerial 26 photography. It is recommended that the DWR wells database be consulted for an 27 estimate of abandoned wells that have not been destroyed, so that these old wells are not 28 conduits for flood waters to the groundwater. A formal well canvas is recommended. 29 Floodproofed wells would be provided with year-round vehicular access via a raised 30 roadbed across the floodplain. The roadbed could include multiple culverts to support 31 floodplain connectivity, depending on the length of the access road and its effect on 32 floodplain flows.
33 Other Utilities 34 Other infrastructure was identified within the impacted areas. However, costs were not 35 developed for this infrastructure at this time. Other facilities include: high voltage 36 transmission lines, gas lines, and water pipelines. High voltage transmission lines are 37 assumed to be high enough to not be impacted. Gas lines are typically attached to 38 bridges or buried below the river when crossing the river and were assumed not to require 39 relocation. As such, no costs for gas line relocation or replacement would be involved, 40 but there could be mitigation required when crossing a gas line with a levee depending on 41 the depth of cover. Water pipelines were quantified from existing maps and discussions 42 with landowners. It was assumed that pipelines will be abandoned in place and no cost is
Mendota Pool Bypass and Reach 2B Improvements Project 7-8 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 involved. Depending on the improvements and grading to be done in the floodplains, 2 there may in fact be a cost for the removal of at least some of the pipelines.
3 Replacement of San Mateo Avenue crossing 4 The San Mateo Avenue crossing is located at approximately RM 211.8, upstream of all 5 the Bypass Initial Alternatives, and consequently within the Floodplain Initial 6 Alternatives area. All Floodplain Initial Alternatives include replacement of the San 7 Mateo Avenue crossing with a box culvert design (see discussion in Section 7.3.3).
8 Levee protection 9 Each Floodplain Initial Alternative generally provides a minimum 300-foot buffer 10 between the existing channel and the proposed levee, where possible. For locations where 11 the 300-foot buffer was not included, erosion protection for the levee in the form of 12 revetment would be included. The revetment would be riprap material covered by soil 13 and then planted to provide a vegetated surface. Locations that require revetment include 14 areas where the 300-foot buffer was not included due to the proximity of existing 15 infrastructure, near the proposed structures, and along river bends less than 300 feet from 16 the levee.
17 Lone Willow Slough Fish Screen 18 Lone Willow Slough connects to the river at approximately RM 215.9 just downstream of 19 the Chowchilla Bifurcation Structure. All Floodplain Initial Alternatives include 20 construction of a fish screen at this diversion (see discussion in Section 7.3.2).
21 Land Acquisition 22 The approximate amount of additional lands to be acquired to accommodate the 23 floodplain, levees, and structures was quantified based on parcel data in shapefile format 24 from Fresno and Madera counties. Since portions of parcels outside the project area may 25 not be as easily utilized by the land owners, the entire parcels were considered in the land 26 acquisition costs for the Floodplain Initial Alternatives.
27 Construction Considerations 28 It was assumed that nuisance water will be in the San Mateo Avenue Crossing 29 construction site and that installation of coffer dams will be required around portions of 30 the work. Since a portion of the existing crossing is private (not a public road), it was 31 assumed that access could be closed during construction. Construction will be timed (July 32 1 to November 1) so that the lesser Restoration Flows (5 to 195 cfs) can be routed around 33 the structure during construction. At high flows water will flow over the structure, in 34 addition to through the proposed culverts. To protect the structure during high flows, the 35 proposed fill will be enclosed in concrete and cutoff walls and riprap are included to 36 prevent damage to the structure during over topping flows.
37 It was assumed that installation of coffer dams will be required around portions of the 38 Chowchilla Fish Ladder. In addition, portions of the existing Chowchilla control 39 structure will need to be demolished (portion of the roadway, and wing wall) in order to 40 construct the fish ladder.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-9 – October 2012 San Joaquin River Restoration Program
1 7.1.2 FP-1 2 Floodplain Initial Alternative FP-1 represents the narrowest floodplain in the range of 3 Initial Alternatives with an average floodplain width of approximately 2,340 feet. 4 Floodplain Initial Alternative FP-1 provides the least floodplain acreage, but also requires 5 the least amount of land acquisition. Table 7-1 lists the quantities of levee construction, 6 relocations, and land acquisition included in this Initial Alternative. Table 7-2, Table 7-3, 7 and Table 7-4 for the costs, benefits, and impacts data used in the evaluation.
8 Fish Habitat and Passage 9 Floodplain Initial Alternative FP-1 provides the least amount of floodplain and the least 10 amount of rearing habitat of all the alternatives at the FSRAF (2,500 cfs as described in 11 Section 6.2.2). The limited floodplain width results in low acreages of very shallow 12 water habitat and as flows increase above 3,000 cfs very shallow water habitat is 13 progressively diminished down to insignificant levels (approximately 5 acres at 4,500 14 cfs) because the entire floodplain is inundated and flows are up against the levees. There 15 are no up or downstream fish passage issues associated with this alternative.
16 Habitat Restoration 17 FP-1 is the narrowest Floodplain Initial Alternative. The constricted conditions will result 18 in the deepest inundation depths and poor quality floodplain. The extent of the anticipated 19 vegetation alliances in this alternative is limited by the narrow corridor. The grass- 20 dominated alliances, which produce the maximum food benefits for salmon, would be 21 located primarily in the upstream, widest part of the reach where two large meander loops 22 and a portion of an existing orchard north of them will be enclosed by the proposed 23 levees. The higher, flat parts of the meander loops would likely be dominated by 24 Saltgrass Flats. The adjacent existing wetland areas within the loops could be preserved 25 or enhanced by additional wetland species plantings and invasive species removal. The 26 middle and lower portions of the reach under this Initial Alternative would primarily 27 maintain the existing vegetation. Additional restoration work could focus on the re- 28 establishment of the Sandbar Willow Thicket, Black Willow Thicket, Oregon Ash 29 Groves and Riparian Bank Herbs. Because of the requirement that there be no woody 30 species on the levees, the riverside levee banks could be planted with plants from the 31 California Mugwort Brush and Creeping Rye Grassland. Low-lying areas outside of the 32 main river channel, with stagnant or slowly moving water that may be quite deep during 33 high flows could be planted with Buttonbush Thicket or California Bulrush Marsh.
34
Mendota Pool Bypass and Reach 2B Improvements Project 7-10 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-1. 2 FP-1 Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 7.7 miles 5.9 miles Average Levee Height 5.8 feet 6.3 feet Fill Volume 350,000 cubic yards 270,000 cubic yards Relocations Electrical Distribution 20,272 feet Facility 1 Gas Transmission 5,029 feet Groundwater Well 19 Water Pipeline 15,976 feet Lift Pump 5 Canal 26,668 feet Power Pole 68 Confluence 1 Monitoring Well - Culvert 1 Regulating Reservoir - Diversion 1 Abandoned Well - Barn/Shed - Land Acquisition1 Total 1,076 acres 3 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
4 Table 7-2. 5 FP-1 Implementation/Technical Feasibility Evaluation Data Units of Categories Factors Criteria FP-1 Measure Capital Improvement Costs dollars $194,430,000 Upfront Costs Land Costs dollars $15,300,000 Costs Subtotal dollars $209,730,000 Long-Term Costs O&M dollars/year $606,000 Time to Build Timeline Construction months 40
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-11 – October 2012 San Joaquin River Restoration Program
1 Table 7-3. 2 FP-1 Objectives/Benefits Achievement Evaluation Data Units of Categories Factors Criteria FP-1 Measure rating: 1 Shallow Water Habitat Quality (poor), 3 1 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres 373 2,500 cfs) number of Passage Artificial structures in migratory path 2 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 12 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 3 Salmon structures Wetlands and other waters of the U.S acres of 451.3 area hydric soils Sensitive vegetation alliance extent acres 817.0 Button willow thickets acres 36.8 California bulrush marsh acres 46.9 California mugwort brush acres 96.4 Creeping rye grass turfs acres 49.3 Vegetation Riparian banks forbes and herbs acres 89.5 Salt grass flats acres 148.0 Fremont cottonwood forest acres 14.6 Oregon ash groves acres 35.7 Sandbar willow thickets acres 124.9 Habitat Black willow thickets acres 97.9 Restoration Exist. sensitive vegetation alliance acres 76.9 preservation Wildlife habitat extent acres 740.1 Freshwater emergent wetland acres 136.4 Riparian scrub acres 133.2 Valley foothill riparian acres 50.3 Wet herbaceous acres 197.4 Wildlife Willow scrub acres 222.8 Special-status species habitat extent acres 581.4 Greater sandhill crane acres 333.8 Swainson's hawk acres 247.6 Net change in wildland extent acres 395.6 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $1,935,000 protection cost)
Mendota Pool Bypass and Reach 2B Improvements Project 7-12 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-4. 2 FP-1 Impacts Evaluation Data Units of Categories Factors Criteria FP-1 Measure Acres of land in which groundwater levels acres 490 rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres 580 rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 400.5 Alfalfa acres 0.0 Almond acres 213.0 Crop Acreage Grapes acres 64.6 Socioeconomics Other Row Crop acres 0.0 and Economics Palm acres 9.7 Pistachio acres 113.3 Agricultural Reduction in annual agricultural dollars $2,339,259 Economic Impacts production values Wetland Impacts acres 66.4 Freshwater Emergent Wetland acres 0.0 Freshwater Forested/Shrub Wetland acres 41.3 Riverine acres 25.1 Sensitive Vegetation Alliance Direct acres 48.0 Impacts Alkali heath marsh acres 0.0 Arrow weed thickets acres 0.1 Black willow thickets acres 19.9 Blue elderberry stands acres 16.3 Special Status Button willow thickets acres 0.1 Vegetation California bulrush marsh acres 0.5 California rose briar patches acres 4.4 Creeping rye grass turfs acres 0.2 Fremont cottonwood forest acres 3.6 Oregon ash groves acres 0.9 Pale spike rush marshes acres 0.0 Salt grass flats acres 0.9 Environmental Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.0 Tar plant fields acres 1.0 Yerba mansa meadows acres 0.0 Special status wildlife habitat impacts acres 220.9 Blunt-nosed leopard lizard acres 11.5 Fairy shrimp acres 2.3 Fresno kangaroo rat acres 21.4 Giant garter snake acres 35.0 Special Status Wildlife Greater sandhill crane acres 56.0 San Joaquin kit fox acres 30.4 Swainson's hawk acres 48.0 Valley elderberry longhorn beetle acres 16.3 number of Valley elderberry longhorn beetle 270 elderberry shrubs number of listed Historic Properties Potentially Effected 3 Cultural and properties Historical ranking: 1 (very Resources Buried Deposits Sensitivity 4 low)-5 (very high)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-13 – October 2012 San Joaquin River Restoration Program
1
2 7.1.3 FP-2 3 Floodplain Initial Alternative FP-2 is the second narrowest floodplain in the range of 4 Initial Alternatives with an average floodplain width of approximately 3,070 feet. Table 5 7-5 lists the quantities of levee construction, relocations, and land acquisition included in 6 this Initial Alternative. See Table 7-6, Table 7-7, Table 7-8 for the costs, benefits, and 7 impacts data used in the evaluation.
8 Fish Habitat and Passage 9 Floodplain Initial Alternative FP-2 provides a moderate amount of floodplain habitat 10 resulting in sufficient acres of the very shallow water habitat for primary production as 11 well as sufficient acres of habitat that supporting direct rearing at the FSRAF. FP-2 also 12 retains very shallow water habitat at flows up to 4,500 cfs. There are no up or 13 downstream fish passage issues associated with this alternative.
14 Habitat Restoration 15 Floodplain Initial Alternative FP-2 includes a somewhat wider floodplain than FP-1. This 16 alternative incorporates larger areas of land between the meander loops and provides a 17 good quality floodplain with slightly larger area of protected existing habitat. The extent 18 of the anticipated vegetation alliances in this alternative is sufficient to support beneficial 19 salmonid habitat. The grass-dominated vegetation alliances, which produce the maximum 20 food benefits for salmon, would likely be well distributed along the reach, with the 21 largest segments of grasslands in the upstream portion of the reach. The higher, flat parts 22 of all of the meander loop areas would likely be dominated by Saltgrass Flats. The 23 adjacent existing wetland areas within the loops could be preserved or enhanced by 24 additional wetland species plantings and removal of numerous invasive species. In 25 addition to the Saltgrass Flats, the middle and lower portions of the reach under this 26 alternative could include predominantly Sandbar Willow Thickets, California Mugwort 27 Brush, and Black Willow Thickets. Additional restoration work could focus on the re- 28 establishment of the Riparian Bank Herbs, California Bulrush Marsh, Button Willow 29 Thickets, Oregon Ash Groves, Creeping Rye Grasslands, and Fremont Cottonwood 30 Forests. The riverside of the proposed levee banks could be planted with plant species 31 from the California Mugwort Brush and Creeping Rye Grassland alliances. Low-lying 32 areas outside of the main river channel, with stagnant or slowly moving water that may 33 be deep during high flows could be planted with Buttonbush Thicket or California 34 Bulrush Marsh. This alternative could include a considerably larger area of the Fremont 35 Cottonwood Forest than FP-1. The Fremont Cottonwood Forest is considered one of the 36 most important riparian plant communities in California because of the height of the 37 cottonwood trees and the “gallery forest” effect, with several stories of branches above 38 the riparian plain which provide habitat for the largest diversity of bird species in 39 California (Barbour 2007). Additionally, because of the fast growth and its soft and 40 brittle wood, the cottonwood is considered to be a good source of large woody debris and 41 organic matter within the riverine channel.
Mendota Pool Bypass and Reach 2B Improvements Project 7-14 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-5. 2 FP-2 Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 6.3 miles 4.9 miles Average Levee Height 5.5 feet 5.0 feet Fill Volume 230,000 cubic yards 160,000 cubic yards Relocations Electrical Distribution 21,409 feet Facility 1 Gas Transmission 7,613 feet Groundwater Well 19 Water Pipeline 22,569 feet Lift Pump 5 Canal 27,191 feet Power Pole 72 Confluence 1 Monitoring Well - Culvert 1 Regulating Reservoir - Diversion 1 Abandoned Well - Barn/Shed - Land Acquisition1 Total 1,465 acres 3 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
4 Table 7-6. 5 FP-2 Implementation/Technical Feasibility Evaluation Data Units of Categories Factors Criteria FP-2 Measure Capital Improvement Costs dollars $192,480,000 Upfront Costs Land Costs dollars $19,800,000 Costs Subtotal dollars $212,280,000 Long-Term Costs O&M dollars/year $646,000 Time to Build Timeline Construction months 40
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-15 – October 2012 San Joaquin River Restoration Program
1 Table 7-7. 2 FP-2 Objectives/Benefits Achievement Evaluation Data Units of Categories Factors Criteria FP-2 Measure rating: 1 Shallow Water Habitat Quality (poor), 3 3 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres 482 2,500 cfs) number of Passage Artificial structures in migratory path 2 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 12 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 3 Salmon structures Wetlands and other waters of the U.S acres of 518.3 area hydric soils Sensitive vegetation alliance extent acres 1208.1 Button willow thickets acres 70.9 California bulrush marsh acres 72.2 California mugwort brush acres 117.8 Creeping rye grass turfs acres 46.6 Vegetation Riparian banks forbes and herbs acres 90.9 Salt grass flats acres 248.4 Fremont cottonwood forest acres 38.9 Oregon ash groves acres 67.2 Sandbar willow thickets acres 261.9 Habitat Black willow thickets acres 114.5 Restoration Exist. sensitive vegetation alliance acres 78.7 preservation Wildlife habitat extent acres 1129.4 Freshwater emergent wetland acres 163.2 Riparian scrub acres 188.7 Valley foothill riparian acres 106.1 Wet herbaceous acres 295.1 Wildlife Willow scrub acres 376.4 Special-status species habitat extent acres 859.4 Greater sandhill crane acres 458.2 Swainson's hawk acres 401.2 Net change in wildland extent acres 756.3 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $1,123,000 protection cost)
Mendota Pool Bypass and Reach 2B Improvements Project 7-16 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-8. 2 FP-2 Impacts Evaluation Data Units of Categories Factors Criteria FP-2 Measure Acres of land in which groundwater levels acres 330 rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres 390 rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 658.7 Alfalfa acres 0.0 Almond acres 340.4 Crop Acreage Grapes acres 76.1 Socioeconomics Other Row Crop acres 0.0 and Economics Palm acres 9.7 Pistachio acres 232.5 Agricultural Reduction in annual agricultural dollars $3,630,735 Economic Impacts production values Wetland Impacts acres 64.6 Freshwater Emergent Wetland acres 0.0 Freshwater Forested/Shrub Wetland acres 40.4 Riverine acres 24.1 Sensitive Vegetation Alliance Direct acres 48.2 Impacts Alkali heath marsh acres 0.0 Arrow weed thickets acres 0.2 Black willow thickets acres 18.5 Blue elderberry stands acres 16.4 Special Status Button willow thickets acres 0.1 Vegetation California bulrush marsh acres 0.6 California rose briar patches acres 4.4 Creeping rye grass turfs acres 0.0 Fremont cottonwood forest acres 3.0 Oregon ash groves acres 0.9 Pale spike rush marshes acres 0.0 Salt grass flats acres 0.9 Environmental Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.0 Tar plant fields acres 3.1 Yerba mansa meadows acres 0.0 Special status wildlife habitat impacts acres 202.0 Blunt-nosed leopard lizard acres 11.1 Fairy shrimp acres 2.3 Fresno kangaroo rat acres 21.0 Giant garter snake acres 37.2 Special Status Wildlife Greater sandhill crane acres 52.2 San Joaquin kit fox acres 24.1 Swainson's hawk acres 37.7 Valley elderberry longhorn beetle acres 16.4 number of Valley elderberry longhorn beetle 273 elderberry shrubs number of listed Historic Properties Potentially Effected 3 Cultural and properties Historical ranking: 1 (very Resources Buried Deposits Sensitivity 4 low)-5 (very high)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-17 – October 2012 San Joaquin River Restoration Program
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2 7.1.4 FP-3 3 Floodplain Initial Alternative FP-3 has the same levee alignments as Floodplain Initial 4 Alternative FP-2 (average floodplain width of approximately 3,070 feet) but includes 5 grading on the floodplain to establish greater heterogeneity of water depths on the 6 floodplain. A variety of floodplain depths potentially provides more habitat appropriate 7 for rearing salmonids. Table 7-9 lists the quantities of levee construction, relocations, and 8 land acquisition included in this Initial Alternative. See Table 7-10, Table 7-11, and 9 Table 7-12 for the costs, benefits, and impacts data used in the evaluation.
10 While a conceptual grading plan was developed during concept refinement that focused 11 on providing more floodplain connectivity and greater floodplain depths, the quantity and 12 location of floodplain grading should be refined during the next Project stages as an 13 avoidance measure for existing vegetation and habitat.
14 Fish Habitat and Passage 15 Floodplain Initial Alternative FP-3 provides a moderate amount of floodplain habitat 16 resulting in sufficient acres of shallow water habitat for primary production as well as 17 sufficient acres of habitat supporting direct rearing at the FSRAF. FP-3 also retains 18 shallow water habitat at flows up to 4,500 cfs. In addition, grading areas for this 19 alternative increase the amount of floodplain habitat available at lower flows. There are 20 no up or downstream fish passage issues associated with this alternative.
21 Habitat Restoration 22 Floodplain Initial Alternative FP-3 includes the same floodplain acreage as FP-2. The 23 main difference between this alternative and FP-2 is several high flow channels shorting 24 the meander loops. The anticipated vegetation alliances in this alternative could be 25 enriched by additional riparian bank herb communities along the high flow channels. The 26 grass-dominated vegetation alliances, which produce the maximum food benefits for 27 salmon, could be well distributed but their areal extent is slightly lower than in FP-2. The 28 higher, flat parts of all of the meander loop areas would likely be dominated by Saltgrass 29 Flats. The adjacent existing wetland areas within the loops could be preserved or 30 enhanced by additional wetland species plantings and removal of numerous invasive 31 species. In addition to the Saltgrass Flats, the middle and lower portions of the reach 32 under this alternative could include predominantly Sandbar Willow Thickets, California 33 Mugwort Brush and Black Willow Thickets. Additional restoration work could focus on 34 the re-establishment of the Riparian Bank Herbs, California Bulrush Marsh, Button 35 Willow Thickets, Oregon Ash Groves, Creeping Rye Grasslands, and Fremont 36 Cottonwood Forests. The riverside of the proposed levee banks could be planted with 37 plant species from the California Mugwort Brush and Creeping Rye Grassland alliances. 38 Low-lying areas outside of the main river channel, with stagnant or slowly moving water 39 that may be deep during high flows could be planted with Buttonbush Thicket or 40 California Bulrush Marsh.
Mendota Pool Bypass and Reach 2B Improvements Project 7-18 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-9. 2 FP-3 Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 6.3 miles 4.9 miles Average Levee Height 5.5 feet 5.0 feet Fill Volume 230,000 cubic yards 160,000 cubic yards Relocations Electrical Distribution 21,409 feet Facility 1 Gas Transmission 7,613 feet Groundwater Well 19 Water Pipeline 22,569 feet Lift Pump 5 Canal 27,191 feet Power Pole 72 Confluence 1 Monitoring Well - Culvert 1 Regulating Reservoir - Diversion 1 Abandoned Well - Barn/Shed - Land Acquisition1 Total 1,465 acres 3 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
4 Table 7-10. 5 FP-3 Implementation/Technical Feasibility Evaluation Data Units of Categories Factors Criteria FP-3 Measure Capital Improvement Costs dollars $194,780,000 Upfront Costs Land Costs dollars $19,800,000 Costs Subtotal dollars $214,580,000 Long-Term Costs O&M dollars/year $646,000 Time to Build Timeline Construction months 40
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-19 – October 2012 San Joaquin River Restoration Program
1 Table 7-11. 2 FP-3 Objectives/Benefits Achievement Evaluation Data Units of Categories Factors Criteria FP-3 Measure rating: 1 Shallow Water Habitat Quality (poor), 3 3 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres 481 2,500 cfs) number of Passage Artificial structures in migratory path 2 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 12 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 3 Salmon structures Wetlands and other waters of the U.S acres of 518.3 area hydric soils Sensitive vegetation alliance extent acres 1208.7 Button willow thickets acres 43.0 California bulrush marsh acres 72.2 California mugwort brush acres 114.5 Creeping rye grass turfs acres 47.1 Vegetation Riparian banks forbes and herbs acres 117.1 Salt grass flats acres 218.8 Fremont cottonwood forest acres 38.6 Oregon ash groves acres 61.8 Sandbar willow thickets acres 277.0 Habitat Black willow thickets acres 140.8 Restoration Exist. sensitive vegetation alliance acres 77.6 preservation Wildlife habitat extent acres 1131.1 Freshwater emergent wetland acres 189.4 Riparian scrub acres 298.4 Valley foothill riparian acres 100.4 Wet herbaceous acres 265.9 Wildlife Willow scrub acres 277.0 Special-status species habitat extent acres 821.6 Greater sandhill crane acres 455.3 Swainson's hawk acres 366.3 Net change in wildland extent acres 756.9 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $1,123,000 protection cost)
Mendota Pool Bypass and Reach 2B Improvements Project 7-20 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-12. 2 FP-3 Impacts Evaluation Data Units of Categories Factors Criteria FP-3 Measure Acres of land in which groundwater levels acres 330 rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres 390 rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 658.7 Alfalfa acres 0.0 Almond acres 340.4 Crop Acreage Grapes acres 76.1 Socioeconomics Other Row Crop acres 0.0 and Economics Palm acres 9.7 Pistachio acres 232.5 Agricultural Reduction in annual agricultural dollars $3,630,735 Economic Impacts production values Wetland Impacts acres 66.8 Freshwater Emergent Wetland acres 0.0 Freshwater Forested/Shrub Wetland acres 40.6 Riverine acres 26.2 Sensitive Vegetation Alliance Direct acres 50.0 Impacts Alkali heath marsh acres 0.0 Arrow weed thickets acres 0.2 Black willow thickets acres 19.1 Blue elderberry stands acres 16.6 Special Status Button willow thickets acres 0.2 Vegetation California bulrush marsh acres 0.6 California rose briar patches acres 4.6 Creeping rye grass turfs acres 0.0 Fremont cottonwood forest acres 3.1 Oregon ash groves acres 1.5 Pale spike rush marshes acres 0.0 Salt grass flats acres 0.9 Environmental Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.0 Tar plant fields acres 3.1 Yerba mansa meadows acres 0.0 Special status wildlife habitat impacts acres 204.5 Blunt-nosed leopard lizard acres 11.1 Fairy shrimp acres 2.3 Fresno kangaroo rat acres 21.0 Giant garter snake acres 39.1 Special Status Wildlife Greater sandhill crane acres 52.2 San Joaquin kit fox acres 24.1 Swainson's hawk acres 38.2 Valley elderberry longhorn beetle acres 16.6 number of Valley elderberry longhorn beetle 285 elderberry shrubs number of listed Historic Properties Potentially Effected 3 Cultural and properties Historical ranking: 1 (very Resources Buried Deposits Sensitivity 4 low)-5 (very high)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-21 – October 2012 San Joaquin River Restoration Program
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2 7.1.5 FP-4 3 Floodplain Initial Alternative FP-4 represents the second widest floodplain in the range of 4 Initial Alternatives with an average floodplain width of approximately 4,200 feet. Table 5 7-13 lists the quantities of levee construction, relocations, and land acquisition included 6 in this Initial Alternative. See Table 7-14, Table 7-15, Table 7-16 for the costs, benefits, 7 and impacts data used in the evaluation.
8 Fish Habitat and Passage 9 Floodplain Initial Alternative FP-4 provides sufficient rearing habitat on the floodplain, 10 but at 2,500 cfs, there are about equal acres of shallow water habitat and direct rearing 11 habitat, and about half of the shallow water habitat is very shallow water habitat (less 12 than 0.5 feet deep). This results in fair quality shallow water habitat. As flows increase 13 above 2,500 cfs, the proportion of shallow water habitat decreases; at 3,000 cfs it is about 14 25% of the amount of rearing habitat; at 4,000 cfs it is about 10% of rearing habitat. 15 There are no up or downstream fish passage issues associated with this alternative.
16 Habitat Restoration 17 Floodplain Initial Alternative FP-4 is the second largest alternative. Because of the areal 18 extent of the floodplain, the inundation depth will be relatively shallow and the quality of 19 the floodplain average. The grass-dominated vegetation alliances, which produce the 20 maximum food benefits for salmon, could be more than twice as large as those in FP-2 21 and FP-3. All of the elevated areas of the meander loops would likely be dominated by 22 Saltgrass Flats. The existing wetland areas within the loops could be preserved or 23 enhanced by additional wetland species plantings and removal of numerous invasive 24 species. The lower lying portions of the reach in this alternative could be planted with the 25 Button Willow Thicket vegetation alliance. Because of the wide floodplain and the 26 slowly moving water, the extent of this vegetation alliance could almost quadruple 27 compared to alternatives FP-2 and FP-3. The extent of black willow thicket and 28 California mugwort brush could increase considerably also. The riverside levee banks 29 could be planted with plant species from the California Mugwort Brush and Creeping 30 Rye Grassland. Since creeping wild rye (Leymus triticoides) is a facultative wetland 31 species that thrives in the upper parts of riparian areas, the extent of Creeping Rye 32 Grassland could more than double compared to FP-2 and FP-3 because FP-4 has 33 shallower inundation depths.
Mendota Pool Bypass and Reach 2B Improvements Project 7-22 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-13. 2 FP-4 Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 6.0 miles 4.6 miles Average Levee Height 5.3 feet 4.1 feet Fill Volume 230,000 cubic yards 120,000 cubic yards Relocations Electrical Distribution 28,482 feet Facility 1 Gas Transmission 10,441 feet Groundwater Well 26 Water Pipeline 30,320 feet Lift Pump 6 Canal 28,839 feet Power Pole 99 Confluence 0 Monitoring Well 1 Culvert 1 Regulating Reservoir - Diversion 2 Abandoned Well - Barn/Shed - Land Acquisition1 Total 2,011 acres 3 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
4 Table 7-14. 5 FP-4 Implementation/Technical Feasibility Evaluation Data Units of Categories Factors Criteria FP-4 Measure Capital Improvement Costs dollars $218,110,000 Upfront Costs Land Costs dollars $27,300,000 Costs Subtotal dollars $245,410,000 Long-Term Costs O&M dollars/year $721,000 Time to Build Timeline Construction months 45
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-23 – October 2012 San Joaquin River Restoration Program
1 Table 7-15. 2 FP-4 Objectives/Benefits Achievement Evaluation Data Units of Categories Factors Criteria FP-4 Measure rating: 1 Shallow Water Habitat Quality (poor), 3 2 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres 585 2,500 cfs) number of Passage Artificial structures in migratory path 2 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 12 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 3 Salmon structures Wetlands and other waters of the U.S acres of 751.6 area hydric soils Sensitive vegetation alliance extent acres 1752.2 Button willow thickets acres 167.2 California bulrush marsh acres 72.2 California mugwort brush acres 163.0 Creeping rye grass turfs acres 97.6 Vegetation Riparian banks forbes and herbs acres 89.0 Salt grass flats acres 483.3 Fremont cottonwood forest acres 51.1 Oregon ash groves acres 63.5 Sandbar willow thickets acres 318.7 Habitat Black willow thickets acres 169.1 Restoration Exist. sensitive vegetation alliance acres 77.5 preservation Wildlife habitat extent acres 1674.7 Freshwater emergent wetland acres 161.2 Riparian scrub acres 330.1 Valley foothill riparian acres 114.6 Wet herbaceous acres 580.9 Wildlife Willow scrub acres 487.9 Special-status species habitat extent acres 1437.6 Greater sandhill crane acres 742.1 Swainson's hawk acres 695.5 Net change in wildland extent acres 1299.9 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $315,000 protection cost)
Mendota Pool Bypass and Reach 2B Improvements Project 7-24 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-16. 2 FP-4 Impacts Evaluation Data Units of Categories Factors Criteria FP-4 Measure Acres of land in which groundwater levels acres 300 rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres 360 rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 1,159.2 Alfalfa acres 0.0 Almond acres 544.7 Crop Acreage Grapes acres 169.6 Socioeconomics Other Row Crop acres 0.0 and Economics Palm acres 9.7 Pistachio acres 435.2 Agricultural Reduction in annual agricultural dollars $6,084,658 Economic Impacts production values Wetland Impacts acres 62.9 Freshwater Emergent Wetland acres 0.0 Freshwater Forested/Shrub Wetland acres 40.1 Riverine acres 22.8 Sensitive Vegetation Alliance Direct acres 48.6 Impacts Alkali heath marsh acres 0.0 Arrow weed thickets acres 0.2 Black willow thickets acres 18.1 Blue elderberry stands acres 16.3 Special Status Button willow thickets acres 0.1 Vegetation California bulrush marsh acres 1.0 California rose briar patches acres 4.4 Creeping rye grass turfs acres 0.0 Fremont cottonwood forest acres 3.8 Oregon ash groves acres 0.8 Pale spike rush marshes acres 0.0 Salt grass flats acres 0.9 Environmental Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.0 Tar plant fields acres 2.9 Yerba mansa meadows acres 0.0 Special status wildlife habitat impacts acres 199.6 Blunt-nosed leopard lizard acres 10.9 Fairy shrimp acres 2.3 Fresno kangaroo rat acres 20.8 Giant garter snake acres 38.9 Special Status Wildlife Greater sandhill crane acres 48.4 San Joaquin kit fox acres 24.2 Swainson's hawk acres 37.9 Valley elderberry longhorn beetle acres 16.3 number of Valley elderberry longhorn beetle 270 elderberry shrubs number of listed Historic Properties Potentially Effected 3 Cultural and properties Historical ranking: 1 (very Resources Buried Deposits Sensitivity 4 low)-5 (very high)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-25 – October 2012 San Joaquin River Restoration Program
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2 7.1.6 FP-5 3 Floodplain Initial Alternative FP-5 represents the widest floodplain in the range of Initial 4 Alternatives with an average floodplain width of approximately 5,600 feet. Floodplain 5 Initial Alternative FP-5 provides the most floodplain acreage, but also requires the most 6 amount of land acquisition. Table 7-17 lists the quantities of levee construction, 7 relocations, and land acquisition included in this Initial Alternative. See Table 7-18, 8 Table 7-19, and Table 7-20 for the costs, benefits, and impacts data used in the 9 evaluation.
10 Fish Habitat and Passage 11 Floodplain Initial Alternative FP-5 provides more shallow water habitat than direct 12 rearing habitat at flows of about 2,500 cfs, and about half of the shallow water habitat is 13 very shallow water habitat (less than 0.5 feet deep). As flows increase above 2,500 cfs, 14 the proportion of shallow water habitat decreases; at 3,000 cfs it is nearly 80% of the 15 amount of rearing habitat; at 4,000 cfs it is about 40% of rearing habitat. In both higher 16 flow cases, very shallow water habitat makes up a significantly proportion (40-60%) of 17 the total shallow water habitat. There are no up or downstream fish passage issues 18 associated with this alternative.
19 Based on a review of the floodplain modeling, an additional negative feature of FP-5 is 20 the potential to strand fish. The land adjacent to the Reach 2B slopes away from the 21 channel and towards the proposed levee; hence, when FP-5 floods up, water would flow 22 overland toward the levee. This would not be a problem during flood up but it becomes a 23 problem during flow recession. As flows recede, inundated areas adjacent to the levee 24 become disconnected from the channel (between 3,500 and 3,000 cfs). Fish could 25 become stranded in the disconnected floodplain areas. While there is some stranding 26 potential in all the alternatives, there is a much higher potential for it to occur in FP-5 27 because of the extensive levee set back. Grading could be used to connect low-lying 28 areas to the main channel to provide escape routes, but the long distance between levee 29 and channel in FP-5 would likely result in slower velocities and higher siltation in the 30 potential escape routes, and the grading would likely require periodic maintainenance.
31 Habitat Restoration 32 Floodplain Initial Alternative FP-5 is the largest alternative. Because of the areal extent 33 of the floodplain, the inundation depth would be very shallow and the quality of the 34 floodplain poor. The grass-dominated vegetation alliances, which produce the maximum 35 food benefits for salmon, would however be very large. All of the higher areas of the 36 meander loops would likely be dominated by Saltgrass Flats. The existing wetland areas 37 within the loops could be preserved or enhanced by additional wetland species plantings 38 and removal of numerous invasive species. The lower lying portions of the reach in this 39 alternative could be planted with Button Willow Thicket and California Bulrush Marsh. 40 The Black Willow Thicket and California Mugwort Brush could be the next largest 41 vegetation alliances. The riverside of the proposed levee banks could be planted with 42 plant species from the California Mugwort Brush and Creeping Rye Grassland. Since 43 creeping wildrye (Leymus triticoides) is a facultative wetland species that thrives in the
Mendota Pool Bypass and Reach 2B Improvements Project 7-26 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 upper parts of riparian areas, the extent of Creeping Rye Grassland could almost double 2 compared to FP-4 because of the shallower inundation depths. This alternative could 3 include a very large Fremont Cottonwood Forest area that would be almost four times as 4 large as the area of this vegetation alliance in FP-4.
5 Table 7-17. 6 FP-5 Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 6.4 miles 4.6 miles Average Levee Height 5.5 feet 3.9 feet Fill Volume 250,000 cubic yards 120,000 cubic yards Relocations Electrical Distribution 46,148 feet Facility 1 Gas Transmission 13,568 feet Groundwater Well 36 Water Pipeline 54,558 feet Lift Pump 8 Canal 40,922 feet Power Pole 170 Confluence 0 Monitoring Well 2 Culvert 1 Regulating Reservoir 3 Diversion 2 Abandoned Well 2 Barn/Shed - Land Acquisition1 Total 2,699 acres 7 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
8 Table 7-18. 9 FP-5 Implementation/Technical Feasibility Evaluation Data Units of Categories Factors Criteria FP-5 Measure Capital Improvement Costs dollars $266,900,000 Upfront Costs Land Costs dollars $36,300,000 Costs Subtotal dollars $303,200,000 Long-Term Costs O&M dollars/year $846,000 Time to Build Timeline Construction months 52
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-27 – October 2012 San Joaquin River Restoration Program
1 Table 7-19. 2 FP-5 Objectives/Benefits Achievement Evaluation Data Units of Categories Factors Criteria FP-5 Measure rating: 1 Shallow Water Habitat Quality (poor), 3 1 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres 762 2,500 cfs) number of Passage Artificial structures in migratory path 2 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 12 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 3 Salmon structures Wetlands and other waters of the U.S acres of 980.4 area hydric soils Sensitive vegetation alliance extent acres 2432.5 Button willow thickets acres 240.4 California bulrush marsh acres 76.5 California mugwort brush acres 201.3 Creeping rye grass turfs acres 182.4 Vegetation Riparian banks forbes and herbs acres 86.4 Salt grass flats acres 578.0 Fremont cottonwood forest acres 198.9 Oregon ash groves acres 118.3 Sandbar willow thickets acres 423.8 Habitat Black willow thickets acres 249.1 Restoration Exist. sensitive vegetation alliance acres 77.3 preservation Wildlife habitat extent acres 2355.2 Freshwater emergent wetland acres 163.0 Riparian scrub acres 446.1 Valley foothill riparian acres 326.5 Wet herbaceous acres 746.7 Wildlife Willow scrub acres 672.9 Special-status species habitat extent acres 1982.9 Greater sandhill crane acres 909.7 Swainson's hawk acres 1073.2 Net change in wildland extent acres 1979.0 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $130,000 protection cost)
Mendota Pool Bypass and Reach 2B Improvements Project 7-28 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-20. 2 FP-5 Impacts Evaluation Data Units of Categories Factors Criteria FP-5 Measure Acres of land in which groundwater levels acres 230 rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres 320 rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 1,797.1 Alfalfa acres 0.0 Almond acres 982.0 Crop Acreage Grapes acres 287.8 Socioeconomics Other Row Crop acres 0.0 and Economics Palm acres 9.7 Pistachio acres 517.6 Agricultural Reduction in annual agricultural dollars $8,988,212 Economic Impacts production values Wetland Impacts acres 64.2 Freshwater Emergent Wetland acres 0.0 Freshwater Forested/Shrub Wetland acres 40.2 Riverine acres 24.0 Sensitive Vegetation Alliance Direct acres 49.3 Impacts Alkali heath marsh acres 0.0 Arrow weed thickets acres 0.2 Black willow thickets acres 18.0 Blue elderberry stands acres 16.3 Special Status Button willow thickets acres 0.1 Vegetation California bulrush marsh acres 0.9 California rose briar patches acres 4.4 Creeping rye grass turfs acres 0.1 Fremont cottonwood forest acres 4.2 Oregon ash groves acres 0.8 Pale spike rush marshes acres 0.0 Salt grass flats acres 0.9 Environmental Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.0 Tar plant fields acres 3.2 Yerba mansa meadows acres 0.0 Special status wildlife habitat impacts acres 200.2 Blunt-nosed leopard lizard acres 11.3 Fairy shrimp acres 2.3 Fresno kangaroo rat acres 21.2 Giant garter snake acres 39.8 Special Status Wildlife Greater sandhill crane acres 46.1 San Joaquin kit fox acres 24.6 Swainson's hawk acres 38.6 Valley elderberry longhorn beetle acres 16.3 number of Valley elderberry longhorn beetle 271 elderberry shrubs number of listed Historic Properties Potentially Effected 3 Cultural and properties Historical ranking: 1 (very Resources Buried Deposits Sensitivity 4 low)-5 (very high)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-29 – October 2012 San Joaquin River Restoration Program
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2 7.2 Bypass Initial Alternatives
3 The Bypass Initial Alternatives include construction of channels and structures capable of 4 conveying 4,500 cfs of Restoration Flows around the Mendota Pool and providing fish 5 passage for salmonids and other native fishes between Reach 2A and Reach 3. The 6 bypass will provide upstream and downstream passage of juvenile Chinook salmon and 7 upstream passage of adult Chinook salmon, as well as passage for other native fishes, 8 while isolating Mendota Pool from Restoration Flows.
9 There were two general approaches used for the bypass. The first involves excavating a 10 channel around the existing Mendota Pool (see Settlement Alignment in Section 7.2.2 11 and Compact Alignment in Section 7.2.3). The second approach involves relocating the 12 Mendota Pool into Fresno Slough and using the old San Joaquin River channel to convey 13 Restoration Flows (see Fresno Slough Dam in Section 7.2.4). Design elements common 14 to each Bypass Initial Alternative include:
15 • Construction of new levees 16 • Removal or partial removal of existing levees 17 • Existing infrastructure relocations or floodproofing 18 • Construction of a bifurcation or control structure with fish screen and ladder 19 • Floodplain and riparian habitat restoration 20 • Columbia Canal relocation and siphon 21 • Land acquisition 22 Additional design elements for the Settlement and Compact alignments include:
23 • Excavation of a channel 24 • Construction of a downstream fish barrier 25 • Construction of in-channel grade control structures 26 Additional design elements for the Fresno Slough Dam include:
27 • Removal of river sediments 28 • Construction of a dam on Fresno Slough 29 • Construction of a water diversion canal 30 • Relocation of portions of the Main Canal and Helm Ditch
31 7.2.1 Elements Common to All Bypass Initial Alternatives 32 The following sections describe the elements that are common to all Bypass Initial 33 Alternatives.
Mendota Pool Bypass and Reach 2B Improvements Project 7-30 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Habitat Restoration 2 For the evaluation, it is assumed that active riparian and floodplain habitat restoration 3 would occur in the Floodplain and Bypass Initial Alternatives similar to the habitat 4 restoration presented for the Initial Floodplain Alternatives.
5 Levees 6 New levees will be constructed along the bypass channel and to connect the bypass 7 channel to the Floodplain Initial Alternatives (extension levees). Proposed levee 8 alignments take into account land parcel boundaries, the 300-foot buffer zone, and 9 appropriate hydraulic and geomorphic transitions between the Floodplain Initial 10 Alternatives and the Bypass Initial Alternatives. The design would be the same as for the 11 Initial Floodplain Alternatives levees.
12 Removal of existing levees 13 All Bypass Initial Alternatives include removal of portions of the existing levees similar 14 to that presented for the Initial Floodplain Alternatives.
15 Existing infrastructure relocations or floodproofing 16 Existing infrastructure such as groundwater wells, pumps, electrical and gas distribution 17 lines, water pipelines, and canals are located in the Project area and will require 18 relocation or floodproofing to protect them from future Restoration Flows and 19 construction of the bypass channel and associated levees and structures. The quantity and 20 extent of relocations varies with each Bypass Initial Alternative. See discussion under 21 the Initial Floodplain Alternatives for more information.
22 7.2.2 Settlement Alignment 23 Bypass Initial Alternative Settlement Alignment will convey 4,500 cfs around the 24 Mendota Pool consistent with the location and layout of the channel as described in 25 exhibits created during the negotiation of the Settlement. This Initial Alternative includes 26 excavating the bypass channel, constructing levees and in-channel structures, relocating 27 or modifying existing infrastructure, and acquiring land. The in-channel structures: 28 bifurcation control structures, grade control structures, fish screen, fish ladder, fish 29 barrier, Columbia Canal Siphon, as well as the Road 10 ½ realignment are discussed in 30 Section 7.3.
31 The bypass channel connects to Reach 3 approximately 1.4 miles downstream from 32 Mendota Dam (approximately RM 203.2), bypasses the Mendota Pool to the north, and 33 connects to Reach 2B approximately 3.1 miles upstream from Mendota Dam 34 (approximately RM 207.7). The bypass channel has a total length of approximately 1.9 35 miles. A siphon under the bypass channel would be constructed to connect the Columbia 36 Canal to the Mendota Pool, and portions of the Canal would be relocated north of the 37 bypass channel.
38 Table 7-21 lists the quantities of levee construction, relocations, and land acquisition 39 included in this Initial Alternative. See Table 7-22, Table 7-23, and Table 7-24 for the 40 costs, benefits, and impacts data used in the evaluation.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-31 – October 2012 San Joaquin River Restoration Program
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2 Figure 7-3. 3 Plan View of Settlement Alignment
4 Fish Habitat and Passage 5 The Bypass Initial Alternative Settlement Alignment includes provision of fish passage 6 for salmonids and other native fish. Specifically, the alternative will provide suitable 7 hydraulic conditions for passage of up-migrating adult salmonids, up- and out-migrating 8 juvenile salmonids, and inter-reach migration of other native fish between Reach 2B and 9 Reach 3. Suitable hydraulic conditions include those conditions which fish are physically 10 capable of passing and do not cause undue stress on the animal (see Fish Passage Design 11 Criteria in Section 5.2.6). The passage features are designed to cause no physical harm 12 and to direct fish into connected migration pathways.
13 The Settlement Alignment includes floodplain and riparian habitat along and directly 14 adjacent to the bypass channel to benefit migrating fish and promote a stable channel and 15 reasonable sediment transport from Reach 2B to Reach 3.
16 The Settlement Alignment also includes several facilities that fish would encounter or 17 need to pass to migrate between Reach 3 and Reach 2B (from downstream to upstream): 18 a fish barrier, nine in-channel drop structures, four fish screen return/bypass outlets, a 19 bifurcation control structure with fish ladder, and a fish screen. Each structure represents 20 a potential stressor for adult salmon and potential predation site for juvenile salmon. 21 However, each structure is designed to perform according to the fish passage design 22 criteria. In addition, the channel and floodplain incorporate riparian plantings to provide 23 cover, woody material, and velocity variability, while the design footprint allows
Mendota Pool Bypass and Reach 2B Improvements Project 7-32 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 sufficient space to incorporate channel structure variability during detailed design. All of 2 which may help to reduce stress and predation.
3 The Settlement Alignment includes a fish barrier at the downstream end of the bypass 4 channel to keep fish from migrating into false migration pathways. Without the barrier, a 5 false migration pathway up to the base of Mendota Dam would be available to fish in all 6 years, and a false migration pathway into Mendota Pool and Fresno Slough (potentially 7 into the King River system) would occur in about one in five years, when the boards are 8 taken out of Mendota Dam to pass Pine Flat flood releases into Reach 3. However, with 9 the barrier, which is designed to accommodate flows up to 4,500 cfs, fish would not be 10 able to migrate to Mendota Dam or enter Mendota Pool, but they would be guided into 11 the bypass channel and Reach 2B.
12 Channel 13 The bypass channel would be a multi-stage channel designed to facilitate fish passage at 14 low flows, channel stability at moderate flows, and contain high flows. The low-flow 15 channel would be designed for a capacity of around 200 cfs and would have a topwidth of 16 approximately 110 feet and a depth of approximately 2 feet. The main channel would be 17 designed for a capacity of around 1,860 cfs (approximately the 2-year annual peak 18 Restoration Flow in Reach 2B) and would have an average topwidth of approximately 19 320 feet and total depth of approximately 6 feet. The floodplain bench would be 20 designed with a shallow cross-slope (approximately 1 percent slope) to allow variable 21 floodplain depths at flows between 1,860 cfs and 4,500 cfs.
22 The channel, designed as an unlined earthen channel, will be approximately 9,800 feet 23 long with a total corridor width of approximately 950 feet and will connect to the river at 24 the downstream end at approximately RM 203.2 and connect at the upstream end at 25 approximately RM 207.7. The average slope of the channel would be approximately 26 0.0004 (approximately 2.1 feet/mile), while the total elevation drop would be 27 approximately 12 feet. A series of grade-control structures are included to achieve the 28 necessary elevation change (see Section 7.3.9). Costs assume that the grade control 29 structures would be constructed with capped and anchored sheet piles. Each grade-control 30 structure will extend across the main channel and key into the overbanks to protect 31 against flanking. Revetment and plantings are included around the structures to further 32 reduce the potential of flanking.
33 Land Acquisition 34 Approximately 710 acres of additional lands will need to be acquired to accommodate the 35 bypass channel, levees and structures. The bypass channel and associated facilities will 36 be constructed within several parcels. Once severed, these lands may not be as easily 37 utilized by the land owners and the entire parcels were considered in the land acquisition 38 costs for this alternative.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-33 – October 2012 San Joaquin River Restoration Program
1 Table 7-21. 2 Settlement Alignment Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length 1.6 miles 1.6 miles Average Levee Height 5.4 feet 5.1 feet Fill Volume 60,000 cubic yards 56,100 cubic yards Relocations Electrical Distribution 1,537 feet Facility - Gas Transmission - Groundwater Well - Water Pipeline - Lift Pump 2 Canal 4,860 feet Power Pole - Confluence 1 Monitoring Well - Culvert - Regulating Reservoir 1 Diversion - Abandoned Well - Barn/Shed - Land Acquisition1 Total 710 acres 3 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
4 Table 7-22. 5 Settlement Alignment Implementation/Technical Feasibility Evaluation Data Settlement Units of Categories Factors Criteria Alignment Measure Bypass Capital Improvement Costs dollars $225,370,000 Upfront Costs Land Costs dollars $13,000,000 Costs Subtotal dollars $238,370,000 Long-Term Costs O&M dollars/year $500,000 Time to Build Timeline Construction months 59
Mendota Pool Bypass and Reach 2B Improvements Project 7-34 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-23. 2 Settlement Alignment Objectives/Benefits Achievement Evaluation Data Settlement Units of Categories Factors Criteria Alignment Measure Bypass rating: 1 Shallow Water Habitat Quality (poor), 3 1 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres 58 2,500 cfs) number of Passage Artificial structures in migratory path 10 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 21 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 11 Salmon structures Wetlands and other waters of the U.S acres of 55.6 area hydric soils Sensitive vegetation alliance extent acres 141.5 Button willow thickets acres 0.0 California bulrush marsh acres 0.0 California mugwort brush acres 18.5 Creeping rye grass turfs acres 20.0 Vegetation Riparian banks forbes and herbs acres 61.1 Salt grass flats acres 15.2 Fremont cottonwood forest acres 0.0 Oregon ash groves acres 0.0 Sandbar willow thickets acres 13.7 Habitat Black willow thickets acres 13.0 Restoration Exist. sensitive vegetation alliance acres 0.0 preservation Wildlife habitat extent acres 141.5 Freshwater emergent wetland acres 61.1 Riparian scrub acres 18.5 Valley foothill riparian acres 0.0 Wet herbaceous acres 35.2 Wildlife Willow scrub acres 26.7 Special-status species habitat extent acres 131.5 Greater sandhill crane acres 96.3 Swainson's hawk acres 35.2 Net change in wildland extent acres 188.1 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $8,455,000 protection cost)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-35 – October 2012 San Joaquin River Restoration Program
1 Table 7-24. 2 Settlement Alignment Impacts Evaluation Data Units of Settlement Categories Factors Criteria Measure Alignment Acres of land in which groundwater levels acres Not estimated rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres Not estimated rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 717.8 Alfalfa acres 190.2 Almond acres 250.3 Crop Acreage Grapes acres 0.0 Socioeconomics Other Row Crop acres 277.3 and Economics Palm acres 0.0 Pistachio acres 0.0 Agricultural Reduction in annual agricultural dollars $1,528,896 Economic Impacts production values Wetland Impacts acres 15.5 Freshwater Emergent Wetland acres 0.0 Freshwater Forested/Shrub Wetland acres 11.8 Riverine acres 3.7 Sensitive Vegetation Alliance Direct acres 9.7 Impacts Alkali heath marsh acres 0.0 Arrow weed thickets acres 0.0 Black willow thickets acres 0.7 Blue elderberry stands acres 0.0 Special Status Button willow thickets acres 0.0 Vegetation California bulrush marsh acres 0.2 California rose briar patches acres 0.0 Creeping rye grass turfs acres 0.0 Fremont cottonwood forest acres 8.8 Oregon ash groves acres 0.0 Pale spike rush marshes acres 0.0 Environmental Salt grass flats acres 0.0 Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.0 Tar plant fields acres 0.0 Yerba mansa meadows acres 0.0 Special status wildlife habitat impacts acres 186.9 Blunt-nosed leopard lizard acres 0.0 Fairy shrimp acres 0.0 Fresno kangaroo rat acres 0.0 Giant garter snake acres 3.4 Special Status Wildlife Greater sandhill crane acres 120.9 San Joaquin kit fox acres 0.0 Swainson's hawk acres 62.6 Valley elderberry longhorn beetle acres 0.0 number of Valley elderberry longhorn beetle 0 elderberry shrubs number of listed Historic Properties Potentially Effected 0 Cultural and properties
Mendota Pool Bypass and Reach 2B Improvements Project 7-36 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
Units of Settlement Categories Factors Criteria Measure Alignment Historical ranking: 1 (very Buried Deposits Sensitivity 1 Resources low)-5 (very high) 1
2 7.2.3 Compact Alignment 3 Bypass Initial Alternative Compact Alignment will convey 4,500 cfs around the Mendota 4 Pool by constructing a channel just south of the Columbia Canal. This Initial Alternative 5 includes excavating the bypass channel, constructing levees and in-channel structures, 6 removing existing levees, relocating or modifying existing infrastructure, and acquiring 7 land. The in-channel structures: bifurcation control structures, grade control structures, 8 fish screen, fish ladder, fish barrier, Columbia Canal Siphon, as well as the Road 10 ½ 9 realignment are discussed in Section 7.3.
10 The bypass channel connects to Reach 3 approximately 0.6 miles downstream from 11 Mendota Dam (approximately RM 204), bypasses the Mendota Pool to the north, and 12 connects to Reach 2B approximately 0.9 miles upstream from Mendota Dam 13 (approximately RM 205.5). The bypass channel has a total length of approximately 0.9 14 miles and is approximately 1.9 miles downstream of the Floodplain Initial Alternatives 15 necessitating extension levees to connect the two. A siphon under the bypass channel 16 would be constructed to connect the Columbia Canal to the Mendota Pool.
17 Table 7-26 lists the quantities of levee construction, relocations, and land acquisition 18 included in this Initial Alternative. See Table 7-26, Table 7-27, Table 7-28 for a summary 19 of the costs, benefits, and impacts data used in the evaluation.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-37 – October 2012 San Joaquin River Restoration Program
1
2 Figure 7-4. 3 Plan View of Compact Alignment
4 Fish Habitat and Passage 5 The Bypass Initial Alternative Compact Alignment includes provision of fish passage for 6 salmonids and other native fish. Specifically, the alternative will provide suitable 7 hydraulic conditions for passage of up-migrating adult salmonids, up- and out-migrating 8 juvenile salmonids, and inter-reach migration of other native fish between Reach 2B and 9 Reach 3. Suitable hydraulic conditions include those conditions which fish are physically 10 capable of passing and do not cause undue stress on the animal (see Fish Passage Design 11 Criteria in Section 5.2.6). The passage features are designed to cause no physical harm 12 and to direct fish into connected migration pathways.
13 The Compact Alignment includes floodplain and riparian habitat along the extension 14 levees and directly adjacent to bypass channel to benefit migrating fish and promote a 15 stable channel and reasonable sediment transport from Reach 2B to Reach 3. However, 16 due to the hydraulics, location, and elevation at the head of the bypass, this alternative 17 reduces the water surface elevation in the river as compared to the Settlement Alignment 18 causing a reduction in inundation acreage upstream of the bypass into the Floodplain 19 Initial Alternatives area.6 The additional rearing habitat provided along the extension
6 The head of the Settlement Alignment was selected as the downstream endpoint of the Floodplain Initial Alternatives, so the hydraulic modeling utilized the hydraulic conditions at the head of the Settlement Bypass as the downstream boundary conditions for the Floodplain Initial Alternatives. The Compact
Mendota Pool Bypass and Reach 2B Improvements Project 7-38 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 levees does not offset the loss of rearing habitat in the floodplains caused by the 2 reduction in inundation. The reduction in inundation acreage is accounted for as negative 3 rearing habitat acreage associated with this Initial Alternative.
4 The Compact Alignment also includes several facilities that fish would encounter or need 5 to pass to migrate between Reach 3 and Reach 2B (from downstream to upstream): a fish 6 barrier, nine in-channel drop structures, four fish screen return/bypass outlets, a 7 bifurcation control structure with fish ladder, and a fish screen. Each structure represents 8 a potential stressor for adult salmon and potential predation site for juvenile salmon. 9 However, each structure is designed to perform according to the fish passage design 10 criteria. In addition, the channel and floodplain incorporate riparian plantings to provide 11 cover, woody material, and velocity variability, while the design footprint allows 12 sufficient space to incorporate channel structure variability during detailed design. All of 13 which may help to reduce stress and predation.
14 The Compact Alignment includes a fish barrier at the downstream end of the bypass 15 channel to keep fish from migrating into false migration pathways. Without the barrier, a 16 false migration pathway up to the base of Mendota Dam would be available to fish in all 17 years, and a false migration pathway into Mendota Pool and Fresno Slough (potentially 18 into the King River system) would occur in about one in five years, when the boards are 19 taken out of Mendota Dam to pass Pine Flat flood releases into Reach 3. However, with 20 the barrier, which is designed to accommodate flows up to 4,500 cfs, fish would not be 21 able to migrate to Mendota Dam or enter Mendota Pool, but they would be guided into 22 the bypass channel and Reach 2B.
23 Channel 24 The bypass channel would be a multi-stage channel designed to facilitate fish passage at 25 low flows, channel stability at moderate flows, and contain high flows. The low-flow 26 channel would be designed for a capacity of around 200 cfs and would have a topwidth of 27 approximately 110 feet and a depth of approximately 2 feet. The main channel would be 28 designed for a capacity of around 1,860 cfs (approximately the 2-year annual peak 29 Restoration Flow in Reach 2B) and would have an average topwidth of approximately 30 320 feet and total depth of approximately 6 feet. The floodplain bench would be 31 designed with a shallow cross-slope (approximately 1 percent slope) to allow variable 32 floodplain depths at flows between 1,860 cfs and 4,500 cfs.
33 The channel, designed as an unlined earthen channel, would be approximately 4,800 feet 34 long with a total corridor width of approximately 950 feet and will connect to the river at 35 the downstream end near approximately RM 204 and connect at the upstream end near 36 approximately RM 205.5. The average slope of the channel would be approximately 37 0.0004 (approximately 2.1 feet/mile), while the total elevation drop would be
Bypass provides different boundary conditions for the Floodplain, so the acreages presented in the tables need to compensate for those differences.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-39 – October 2012 San Joaquin River Restoration Program
1 approximately 12 feet. A series of grade-control structures are included to achieve the 2 necessary elevation change (see Section 7.3.9). Costs assume that the grade control 3 structures would be constructed with capped and anchored sheet piles. Each grade-control 4 structure will extend across the main channel and key into the overbanks to protect 5 against flanking. Revetment and plantings are included around the structures to further 6 reduce the potential of flanking.
7 Land Acquisition 8 Approximately 240 acres of additional lands will need to be acquired to accommodate the 9 bypass channel, levees, and structures. Approximately 282 and 262 acres of additional 10 lands will need to be acquired to accommodate the extension levees and floodplain in the 11 area connecting the Compact Alignment to the Floodplain Initial Alternatives FP-1 and 12 FP-5, respectively. The area includes the channel and floodplain between the existing 13 levees. The area for the FP-1 extension levees and floodplain is larger than that for FP-5, 14 even though FP-5 has a greater setback distance, because a larger portion of land on the 15 downstream end of Reach 2B near RM 207.5 was included in Floodplain Initial 16 Alternative FP-5.
17 Table 7-25. 18 Compact Alignment Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length Bypass Channel 0.9 miles 1.1 miles FP-1 Extension Levees 1.5 miles 1.1 miles FP-5 Extension Levees 1.2 miles 1.1 miles Average Levee Height Bypass Channel 7.0 feet 7.0 feet FP-1 Extension Levees 6.0 feet 5.2 feet FP-5 Extension Levees 5.7 feet 5.0 feet Fill Volume Bypass Channel 51,100 cubic yards 70,500 cubic yards FP-1 Extension Levees 64,100 cubic yards 39,200 cubic yards FP-5 Extension Levees 47,500 cubic yards 36,400 cubic yards Relocations Electrical Distribution 6,683 feet Facility - Gas Transmission - Groundwater Well 2 Water Pipeline 1,254 feet Lift Pump 4 Canal 7,205 feet Power Pole - Confluence - Monitoring Well - Culvert - Regulating Reservoir - Diversion - Abandoned Well - Barn/Shed - Land Acquisition1 522 acres (bypass channel with FP-1 extension levees) Total 502 acres (bypass channel with FP-5 extension levees) 19 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
Mendota Pool Bypass and Reach 2B Improvements Project 7-40 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-26. 2 Compact Alignment Implementation/Technical Feasibility Evaluation Data Compact Units of Categories Factors Criteria Alignment Measure 1 Bypass Capital Improvement Costs dollars $234,970,000 Upfront Costs Land Costs dollars $7,000,000 Costs Subtotal dollars $241,970,000 Long-Term Costs O&M dollars/year $540,000 Time to Build Timeline Construction months 59 3 1 Table shows the worst case (highest costs, least benefits, most impacts) between the bypass channel with FP-1 4 extension levees and bypass channel with FP-5 extension levees.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-41 – October 2012 San Joaquin River Restoration Program
1 Table 7-27. 2 Compact Alignment Objectives/Benefits Achievement Evaluation Data Compact Units of Categories Factors Criteria Alignment Measure 1 Bypass rating: 1 Shallow Water Habitat Quality (poor), 3 1 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres -91 2,500 cfs) number of Passage Artificial structures in migratory path 10 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 21 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 11 Salmon structures Wetlands and other waters of the U.S acres of 97.8 area hydric soils Sensitive vegetation alliance extent acres 218.0 Button willow thickets acres 0.0 California bulrush marsh acres 68.5 California mugwort brush acres 18.0 Creeping rye grass turfs acres 19.1 Vegetation Riparian banks forbes and herbs acres 42.4 Salt grass flats acres 23.2 Fremont cottonwood forest acres 0.0 Oregon ash groves acres 0.0 Sandbar willow thickets acres 1.0 Habitat Black willow thickets acres 16.8 Restoration Exist. sensitive vegetation alliance acres 15.7 preservation Wildlife habitat extent acres 202.1 Freshwater emergent wetland acres 110.8 Riparian scrub acres 18.0 Valley foothill riparian acres 0.0 Wet herbaceous acres 43.9 Wildlife Willow scrub acres 17.6 Special-status species habitat extent acres 210.4 Greater sandhill crane acres 162.0 Swainson's hawk acres 43.9 Net change in wildland extent acres 155.9 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $7,824,000 protection cost) 3 1 Table shows the worst case (highest costs, least benefits, most impacts) between the bypass channel with FP-1 4 extension levees and bypass channel with FP-5 extension levees.
Mendota Pool Bypass and Reach 2B Improvements Project 7-42 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-28. 2 Compact Alignment Impacts Evaluation Data Units of Compact Categories Factors Criteria 1 Measure Alignment Acres of land in which groundwater levels acres Not estimated rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres Not estimated rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 158.3 Alfalfa acres 41.2 Almond acres 24.7 Crop Acreage Grapes acres 0.0 Socioeconomics Other Row Crop acres 92.4 and Economics Palm acres 0.0 Pistachio acres 0.0 Agricultural Reduction in annual agricultural dollars $265,460 Economic Impacts production values Wetland Impacts acres 24.2 Freshwater Emergent Wetland acres 0.0 Freshwater Forested/Shrub Wetland acres 9.4 Riverine acres 14.9 Sensitive Vegetation Alliance Direct acres 22.8 Impacts Alkali heath marsh acres 0.1 Arrow weed thickets acres 0.0 Black willow thickets acres 11.6 Blue elderberry stands acres 0.0 Special Status Button willow thickets acres 0.0 Vegetation California bulrush marsh acres 0.2 California rose briar patches acres 1.0 Creeping rye grass turfs acres 0.6 Fremont cottonwood forest acres 8.9 Oregon ash groves acres 0.1 Pale spike rush marshes acres 0.0 Salt grass flats acres 0.0 Environmental Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.0 Tar plant fields acres 0.2 Yerba mansa meadows acres 0.1 Special status wildlife habitat impacts acres 156.9 Blunt-nosed leopard lizard acres 0.0 Fairy shrimp acres 0.0 Fresno kangaroo rat acres 0.0 Giant garter snake acres 18.3 Special Status Wildlife Greater sandhill crane acres 101.3 San Joaquin kit fox acres 0.0 Swainson's hawk acres 37.4 Valley elderberry longhorn beetle acres 0.0 number of Valley elderberry longhorn beetle 0 elderberry shrubs number of listed Historic Properties Potentially Effected 1 Cultural and properties Historical ranking: 1 (very Resources Buried Deposits Sensitivity 4 low)-5 (very high)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-43 – October 2012 San Joaquin River Restoration Program
1 1 Table shows the worst case (highest costs, least benefits, most impacts) between the bypass channel with FP-1 2 extension levees and bypass channel with FP-5 extension levees. 3
4 7.2.4 Fresno Slough Dam 5 Bypass Initial Alternative Fresno Slough Dam would convey 4,500 cfs around the 6 Mendota Pool by constructing a dam across Fresno Slough which would contain Mendota 7 Pool and using the existing river channel to convey Restoration Flows. This Initial 8 Alternative includes removing a portion of river sediments currently stored behind 9 Mendota Dam, constructing a dam on Fresno Slough, constructing a water delivery canal, 10 constructing levees, removing existing levees, relocating or modifying existing 11 infrastructure, and acquiring land. The in-channel structures: dam, bifurcation control 12 structures, fish screen, fish ladder, Columbia Canal Siphon, and Main Canal and Helm 13 Ditch relocations are discussed in Section 7.3.
14 The Fresno Slough Dam would be located approximately 0.5 miles south of the existing 15 Mendota Dam. Mendota Dam (approximately RM 204.6) is approximately 3.1 miles 16 downstream of the Floodplain Initial Alternatives (approximately RM 207.7) 17 necessitating extension levees along the river to connect the two. Three optional 18 alignments of the water delivery canal to divert water from the San Joaquin River into 19 Mendota Pool were investigated. The North and South Canal alignments would connect 20 to the river upstream of San Mateo Avenue and discharge water to Fresno Slough south 21 of Mendota Dam. The South Canal would discharge via the Little San Joaquin Slough. 22 The Short Canal option would be located directly east of the Fresno Slough Dam. 23 Portions of the Main Canal and Helm Ditch would be relocated to connect them the 24 Mendota Pool, and a siphon under the river would be constructed to connect the 25 Columbia Canal.
26 Table 7-29 lists the quantities of levee construction, relocations, and land acquisition 27 included in this Initial Alternative. See Table 7-30, Table 7-31, Table 7-32 for a summary 28 of the costs, benefits, and impacts data used in the evaluation.
Mendota Pool Bypass and Reach 2B Improvements Project 7-44 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1
2 Figure 7-5. 3 Plan View of Fresno Slough Dam
4 Fish Habitat and Passage 5 The Bypass Initial Alternative Fresno Slough Dam includes provision of fish passage for 6 salmonids and other native fish. Specifically, the alternative will provide suitable 7 hydraulic conditions for passage of up-migrating adult salmonids, up- and out-migrating 8 juvenile salmonids, and inter-reach migration of other native fish between Reach 2B and 9 Reach 3. Suitable hydraulic conditions include those conditions which fish are physically 10 capable of passing and do not cause undue stress on the animal (see Fish Passage Design 11 Criteria in Section 5.2.6). The passage features are designed to cause no physical harm 12 and to direct fish into connected migration pathways.
13 The Fresno Slough Dam includes floodplain and riparian habitat along the extension 14 levees and river channel to benefit migrating fish and promote a stable channel and 15 reasonable sediment transport from Reach 2B to Reach 3. However, due to the 16 hydraulics, location, and elevation of the sill of Mendota Dam, this alternative reduces 17 the water surface elevation in the river causing a reduction in inundation acreage 18 upstream of the Dam into the Floodplain Initial Alternatives area. The additional rearing 19 habitat provided along the extension levees more than offsets the loss of rearing habitat in 20 the floodplains caused by the reduction in inundation area, this Initial Alternative 21 provides additional acreage of rearing habitat.
22 The Fresno Slough Dam also includes several facilities that fish would encounter or need 23 to pass to migrate between Reach 3 and Reach 2B (from downstream to upstream): two 24 in-channel drop structures below Mendota Dam, the sill of Mendota Dam (when boards
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-45 – October 2012 San Joaquin River Restoration Program
1 are out) or a fish ladder at Mendota Dam (when boards are in; Short Canal only), four 2 fish screen return/bypass outlets, a fish screen, and a bifurcation control structure with 3 fish ladder (North and South Canals only). Each structure represents a potential stressor 4 for adult salmon and potential predation site for juvenile salmon. However, each 5 structure is designed to perform according to the fish passage design criteria. In addition, 6 the channel and floodplain incorporate riparian plantings to provide cover, woody 7 material, and velocity variability, while the design footprint allows sufficient space to 8 incorporate channel structure variability during detailed design. All of which may help to 9 reduce stress and predation.
10 The Fresno Slough Dam includes a fish barrier to keep fish from migrating into false 11 migration pathways. False migration pathways will not be available to fish in most years. 12 The only false migration pathway would occur when Pine Flat Reservoir flood releases 13 are coming down the James Bypass into Fresno Slough. During these conditions the 14 gates of Fresno Slough Dam would be open to pass those flows into Reach 3. When the 15 dam gates are open, the barrier would prevent fish from migrating into Fresno Slough and 16 potentially into the King River system were they would be lost to the San Joaquin River. 17 Flood flows in the James Bypass occur in about one in five years.
18 Removal of River Sediments 19 The Fresno Slough Dam would make use of the existing river channel from the end of the 20 Floodplain Initial Alternatives (approximately RM 207.7) down to Mendota Dam 21 (approximately RM 204.6) in order to convey Restoration Flows. Since this portion of 22 the river is currently impounded by Mendota Dam, sediment has filled in the pre- 23 Mendota Dam channel. If left in place once Fresno Slough Dam is implemented, the 24 sediment is expected to erode and establish a new equilibrium slope. The cost of 25 removing sediment for an estimated channel cross-section, equilibrium slope, and length 26 is included in the cost of this Bypass Initial Alternative.
27 Water Delivery Canal 28 The Fresno Slough Dam includes three optional canals for delivering up to 2,500 cfs in 29 water deliveries from the San Joaquin River into Mendota Pool: North Canal, South 30 Canal, and Short Canal. The North and South Canal alignments connect to the river at 31 approximately RM 214.2, upstream of San Mateo Avenue, and discharge water to Fresno 32 Slough at locations approximately 1.8 and 2.3 river miles south of Mendota Dam, 33 respectively. The South Canal discharges via the Little San Joaquin Slough. The Short 34 Canal option would be located directly east of the Fresno Slough Dam. See additional 35 discussion in Section 7.4.2.
36 Land Acquisition 37 Approximately 36 acres of additional lands will need to be acquired to accommodate the 38 dam and other structures. Approximately 340 and 420 acres of additional lands 39 (including the channel and floodplain between the existing levees) will need to be 40 acquired to accommodate the extension levees and floodplain in the area between 41 Mendota Dam and the Floodplain Initial Alternatives FP-1 and FP-5, respectively.
Mendota Pool Bypass and Reach 2B Improvements Project 7-46 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-29. 2 Fresno Slough Dam Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length FP-1 Extension Levees 1.4 miles 2.0 miles FP-5 Extension Levees 1.2 miles 2.5 miles Average Levee Height FP-1 Extension Levees 5.8 feet 5.6 feet FP-5 Extension Levees 4.5 feet 3.5 feet Fill Volume FP-1 Extension Levees 87,500 cubic yards 64,500 cubic yards FP-5 Extension Levees 42,000 cubic yards 68,250 cubic yards Relocations 6,700 feet (FP-1) Electrical Distribution Facility - 12,500 feet (FP-5) Gas Transmission - Groundwater Well 2 (FP-1 & FP-5) Water Pipeline - Lift Pump - 7,200 feet (FP-1) Canal Power Pole - 12,000 feet (FP-5) Confluence - Monitoring Well - Culvert - Regulating Reservoir - Diversion - Abandoned Well - Barn/Shed - Land Acquisition1 376 acres (structures with FP-1 extension levees) Total 456 acres (structures with FP-5 extension levees) 3 Note: This table does not include levee construction, relocations, and land acquisition for the water delivery canals. See 4 Section 7.4.2 and Table 7-34. 5 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands.
6 Table 7-30. 7 Fresno Slough Dam Implementation/Technical Feasibility Evaluation Data Units of Fresno Categories Factors Criteria 1 Measure Slough Dam Capital Improvement Costs dollars $375,990,000 Upfront Costs Land Costs dollars $8,890,000 Costs Subtotal dollars $384,880,000 Long-Term Costs O&M dollars/year $666,000 Time to Build Timeline Construction months 65 8 1 Table shows the worst case (highest costs, least benefits, most impacts) between the structures with FP-1 extension 9 levees and structures with FP-5 extension levees plus the worst case between the water delivery canals.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-47 – October 2012 San Joaquin River Restoration Program
1 Table 7-31. 2 Fresno Slough Dam Objectives/Benefits Achievement Evaluation Data Units of Fresno Categories Factors Criteria 1 Measure Slough Dam rating: 1 Shallow Water Habitat Quality (poor), 3 1 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation at acres 39 2,500 cfs) number of Passage Artificial structures in migratory path 4 Fish Habitat & Conditions for structures Passage Adult Chinook number of Total number of steps at structures 16 Salmon jumps number of Passage Fish Screens along migratory path 1 screens Conditions for Juvenile Chinook number of Potential predation sites artificial 5 Salmon structures Wetlands and other waters of the U.S acres of 101.8 area hydric soils Sensitive vegetation alliance extent acres 251.2 Button willow thickets acres 2.1 California bulrush marsh acres 0.0 California mugwort brush acres 16.2 Creeping rye grass turfs acres 27.8 Vegetation Riparian banks forbes and herbs acres 41.4 Salt grass flats acres 50.5 Fremont cottonwood forest acres 0.0 Oregon ash groves acres 0.0 Sandbar willow thickets acres 23.1 Habitat Black willow thickets acres 72.0 Restoration Exist. sensitive vegetation alliance acres 20.3 preservation Wildlife habitat extent acres 230.9 Freshwater emergent wetland acres 41.4 Riparian scrub acres 16.2 Valley foothill riparian acres 0.0 Wet herbaceous acres 78.3 Wildlife Willow scrub acres 95.1 Special-status species habitat extent acres 197.9 Greater sandhill crane acres 119.6 Swainson's hawk acres 78.3 Net change in wildland extent acres 72.6 Potential to for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars $2,306,000 protection cost) 3 1 Table shows the worst case (highest costs, least benefits, most impacts) between the structures with FP-1 extension 4 levees and structures with FP-5 extension levees plus the worst case between the water delivery canals.
Mendota Pool Bypass and Reach 2B Improvements Project 7-48 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 Table 7-32. 2 Fresno Slough Dam Impacts Evaluation Data Units of Fresno Categories Factors Criteria 1 Measure Slough Dam Acres of land in which groundwater levels acres Not estimated rise above 5-foot monitoring threshold Groundwater Seepage Impacts Acres of land in which groundwater levels acres Not estimated rise above 7-foot monitoring threshold Total Farmland Removed from Production acres 389.1 Alfalfa acres 68.7 Almond acres 81.9 Crop Acreage Grapes acres 83.5 Socioeconomics Other Row Crop acres 167.5 and Economics Palm acres 0.0 Pistachio acres 5.4 Agricultural Reduction in annual agricultural dollars $1,023,146 Economic Impacts production values Wetland Impacts acres 30.4 Freshwater Emergent Wetland acres 7.6 Freshwater Forested/Shrub Wetland acres 10.0 Riverine acres 12.8 Sensitive Vegetation Alliance Direct acres 22.4 Impacts Alkali heath marsh acres 0.4 Arrow weed thickets acres 0.1 Black willow thickets acres 8.9 Blue elderberry stands acres 0.3 Special Status Button willow thickets acres 0.3 Vegetation California bulrush marsh acres 3.7 California rose briar patches acres 2.5 Creeping rye grass turfs acres 0.7 Fremont cottonwood forest acres 4.6 Oregon ash groves acres 0.1 Pale spike rush marshes acres 1.3 Salt grass flats acres 0.3 Environmental Silver bush lupine scrub acres 0.0 Spinescale scrub acres 0.4 Tar plant fields acres 0.7 Yerba mansa meadows acres 0.1 Special status wildlife habitat impacts acres 220.0 Blunt-nosed leopard lizard acres 0.0 Fairy shrimp acres 0.0 Fresno kangaroo rat acres 0.0 Giant garter snake acres 44.9 Special Status Wildlife Greater sandhill crane acres 127.0 San Joaquin kit fox acres 12.4 Swainson's hawk acres 35.4 Valley elderberry longhorn beetle acres 0.3 number of Valley elderberry longhorn beetle 15 elderberry shrubs number of listed Historic Properties Potentially Effected 2 Cultural and properties Historical ranking: 1 (very Resources Buried Deposits Sensitivity 4 low)-5 (very high)
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-49 – October 2012 San Joaquin River Restoration Program
1 1 Table shows the worst case (highest costs, least benefits, most impacts) between the structures with FP-1 extension 2 levees and structures with FP-5 extension levees plus the worst case between the water delivery canals.
3 7.3 Structures Included in the Initial Alternatives
4 More detailed discussion of the structures included in the Initial Alternatives is provided 5 in the following sections. The structures are generally listed from upstream to 6 downstream.
7 7.3.1 Chowchilla Bifurcation Structure Fish Passage Retrofit 8 The San Joaquin control structure at the Chowchilla Bifurcation Structure will not be 9 passable to up-migrating salmon for all flows and flow splits between the river and the 10 Chowchilla Bypass. The undershot gates, sill across the downstream side of the 11 structure, and trash rack on the upstream side contribute to upstream passage difficulties 12 at high, low, and all flows, respectively. It was determined that a fish passage facility 13 would be required for upmigrating salmon to swim into Reach 2A from Reach 2B under 14 most conditions. Appraisal-level design was completed for a fish ladder retrofitted to the 15 side of the San Joaquin control structure.
16 Ladder Design 17 The design of the fish ladder was based on criteria in Anadromous Salmonid Passage 18 Facility Design (NMFS 2008). The size and geometry of the fish ladder was dictated by 19 the flow requirements for juvenile and adult fish. A vertical slot weir ladder design was 20 selected for its ability to accommodate a greater range of water depths (hydraulic head at 21 the upstream and downstream ends), when compared to an ‘ice-harbor’ or ‘pool and 22 chute’ ladder design. The pool dimensions would be governed by the maximum 23 anticipated ladder flow magnitudes.
24 At the ladder upstream exit, a minimum horizontal weir elevation was selected to 25 accommodate up to 9.6 feet of total headwater depth fluctuation. The exit weir is 26 vertically adjustable to control river flow into the ladder. This weir elevation may be 27 controlled either manually or automatically, depending on the level of ladder automation 28 selected in a future design phase.
29 The downstream entrance port of the fish ladder includes a self-sealing mechanically 30 operated vertical slide gate. The purpose of this gate is to control ladder entrance flow 31 and account for variations in the tailwater depth during ladder operation. This slide gate 32 may be either manually or automatically operated, depending on the level of ladder 33 automation selected in a future design phase.
34 A roadway will need to be built over the fish ladder to connect the maintenance road atop 35 the San Joaquin control structure with the levee road on the south side of the river. The 36 roadway would be supported by the vertical concrete walls of the fish ladder. The design 37 may need to be revised to match the size and design and of the Chowchilla Bifurcation 38 Structure.
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1 Portions of the existing San Joaquin control structure, such as the left bank wing wall and 2 a portion of the roadway will need to be demolished before installing the fish ladder.
3 The design flow through the ladder would be based on the fish criteria, and 4 supplementary water may be used to meet attraction flow requirements. The layout and 5 alignment of the ladder and auxiliary features is preliminary and may be updated in a 6 future design phase.
7 7.3.2 Lone Willow Slough Fish Screen 8 Lone Willow Slough connects to the river at approximately RM 215.9 just downstream of 9 the Chowchilla Bifurcation Structure. During high flows, up to 125 cfs of water may be 10 diverted for irrigation from Reach 2B into the Lone Willow Slough. A screen is 11 necessary to prevent fish from entering the canal when flows are being diverted. The 12 fish screen structure consists of a concrete hollow box, with the river side of the box open 13 to river flows and the back of the box fitted with a board guide to control diversion into 14 the irrigation canal. The opening at the riverside includes an automated cleaner system, 15 trash rack and a fish screen to prevent migrating fish from entering the intake. The 16 screen would be designed to meet NMFS 2008 criteria.
17 7.3.3 San Mateo Avenue Crossing 18 The San Mateo Avenue crossing is an existing river crossing located within a public 19 right-of-way in Madera County and on private land in Fresno County at approximately 20 RM 211.8. The crossing transitions from public right-of-way to private land at the center 21 of the river. In order to maintain vehicular access and accommodate increased flow 22 magnitudes, durations, and frequencies associated with Restoration Flows, an improved 23 crossing is included with all Floodplain Initial Alternatives. The crossing will 24 accommodate the increased flows in the river by maintaining the required velocities for 25 proper fish passage for flows up to 4,500 cfs. The crossing would be designed to meet 26 NMFS 2001 and NMFS 2008 passage criteria.
27 The proposed San Mateo Avenue crossing includes installing a low flow or dip crossing 28 with multiple concrete box culverts designed for highway loading. The structure includes 29 armoring along the entrance and exit of the structure as well as along the channel banks 30 in the immediate vicinity of the structure. The armoring is necessary to protect the 31 structure during overtopping flows (greater than approximately 1,500 cfs). Culverts 32 would be embedded below the existing channel bed. Grouted riprap would be placed in 33 the culvert below the existing channel bed to prevent channel scour reaching the floor of 34 the culvert and to create a roughened boundary layer for fish passage. Native bed 35 material would be placed above the grouted riprap up to the existing channel bed to 36 provide passage conditions similar to that which exists in the adjacent natural stream.
37 7.3.4 Mendota Pool Bypass Bifurcation Structure 38 Bifurcation structures would be constructed at the upstream ends of the Settlement 39 Alignment, Compact Alignment, North Canal, and South Canal. Each bifurcation 40 structure consists of two control structures: one across the path of Restoration Flows 41 (bypass channel for the Settlement and Compact alignments and the river for the North 42 and South canals) and one across the path of water deliveries to Mendota Pool (the river
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-51 – October 2012 San Joaquin River Restoration Program
1 for the Settlement and Compact alignments and the water delivery canal for the North 2 and South Canals). The Short Canal has one control structure of similar design.
3 Structures across the path of the Restoration Flows need to accommodate up to 4,500 cfs 4 and consist of multiple bays. Conditions in this control structure would be designed to 5 meet NMFS 2001 and NMFS 2008 passage criteria when flow conditions are amenable. 6 Those across the path of the water deliveries need to accommodate up to 2,500 cfs and 7 also consist of multiple bays. Flow through each bay can be controlled by a radial 8 (Tainter) gate. The gate size would be determined during final design and is based on the 9 design maximum flow.
10 The Restoration Flow path structures include a fish ladder on the right bank side of the 11 structure (see Section 7.3.5), and the water deliveries flow path structures include a fish 12 screen upstream of the structure (see Section 7.3.7). Each control structure is placed in 13 the middle of the channel and has earthen embankments connecting the structure to the 14 levees. A roadway and maintenance/operations platform are provided over each control 15 structure.
16 7.3.5 Mendota Pool Bypass Fish Ladder 17 Each Mendota Pool Bypass control structure across the Restoration Flow path has a fish 18 ladder on the right bank side of the structure. The fish ladder is necessary to provide 19 passage during pool deliveries and for Restoration Flows where passage conditions in the 20 control structure may not be ideal. The design of the fish ladder is the same as that 21 presented for the Chowchilla Bifurcation Structure retrofit in Section 7.3.1.
22 7.3.6 Drive 10 ½ Crossing 23 The Settlement and Compact alignments will cross existing Drive 10 ½, which provides 24 access to the east side of Mendota Dam. The road could be rerouted along the bypass 25 channel levees and cross the bypass channel at the proposed Mendota Pool Bypass 26 bifurcation structure. A road deck would also be provided over the fish ladder adjacent to 27 the bifurcation structure.
28 7.3.7 Mendota Pool Bypass Fish Screen 29 Each control structure across the water deliveries path has a fish screen upstream of the 30 structure. The fish screen is necessary to return out-migrating juvenile salmon to the path 31 of Restoration Flows during pool deliveries.
32 The screen is designed to pass flow up to 2,500 cfs. The fish screen is arranged in four 33 sets of V-shaped configurations. The fish screen facility includes trash racks, stainless 34 steel wedge wire fish screens, flow control baffle systems behind the screens, screen 35 cleaning systems for the trashracks and screens, bypass flow control weirs, fish-friendly 36 pumps, and fish bypass pressure pipelines. The trash racks are installed at the entrance to 37 the screen structures to protect screens from trash, logs, and other large debris.
38 Approach, sweeping, and bypass entrance velocities would be kept within established 39 fish screen criteria (NMFS 2008). Flow through the fish screens may be controlled by 40 baffles behind the fish screens. Cleaning of the screens would be accomplished using an
Mendota Pool Bypass and Reach 2B Improvements Project 7-52 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 automated brush system. Electric power would be needed for fish friendly pumps, if 2 included, and screen cleaning systems. Operation of the fish screens would include 3 methods to reduce predation of juvenile fish (e.g., noise systems to scatter predators, 4 netting, and periodic draining of the screen return pipes).
5 General arrangement and features were configured based on guidelines presented in Fish 6 Protection at Water Diversions (Reclamation 2006). The design shows the outlet of the 7 fish return pipes ending and flowing into the main channel of the Mendota Pool Bypass 8 Channel or river, depending on the Initial Alternative, followed by a section of riprap 9 leading to the low flow channel. Future detailed design will confirm that the outlet 10 structure is appropriate and meets applicable fish criteria.
11 7.3.8 Mendota Dam Fish Barrier 12 Fish exclusion barriers are included in Reach 3 near the downstream ends of the 13 Settlement and Compact alignments to prevent fish from migrating beyond the bypass 14 channel up to the base of Mendota Dam, which during most flows out of Mendota Pool, 15 would be a dead end for fish passage. This would lead to delays in adult salmon 16 migration or potentially death. Although out-migrating fish are not expected to be 17 present downstream from Mendota Dam, the fish barrier would allow juveniles to pass 18 the structure.
19 The exclusion barrier design is a high-flow picket barrier, which is a flow-through 20 structure of closely spaced bars (i.e., pickets) that prevent adult fish from traveling 21 upstream in the river to Mendota Dam at flows up to a combined discharge of 4,500 cfs. 22 The design accounts for a range of flow options from routing the entire 4,500-cfs flow 23 through the structure (flood flows from the James Bypass), to routing a 600-cfs irrigation 24 delivery through the structure with up to 3,900 cfs being routed down the Mendota Pool 25 Bypass Channel, to routing no flow through the structure with up to 4,500 cfs down the 26 Mendota Pool Bypass Channel.
27 For both the Settlement and Compact alignments, the structure will be across the main 28 channel and across the overbanks. The base of the structure will consist of a concrete sill 29 connected to concrete piles, which extend into clay layers. The structure will be 30 approximately 20 feet high in the main channel and 9 feet high in the overbanks. Riprap 31 will be placed 2 feet thick at the entrance and exit of the sill to prevent erosion.
32 Due to challenging river geometry at the outlet of the Settlement Alignment, the average 33 velocity through the structure does not meet the 1.0 fps criteria in Anadromous Salmonid 34 Passage Facility Design (NMFS 2008). The calculated velocity is 1.6 fps. The Compact 35 Alignment fish barrier, however, does meet the NMFS criteria.
36 7.3.9 Mendota Pool Bypass Channel Grade Control Structures 37 For the Settlement and Compact alignments, a series of nine, approximately 1.0-ft high 38 grade-control structures are included within the channel to achieve the necessary 39 elevation change between Reach 2B and Reach 3. Costs assume that the grade control 40 structures would be constructed with capped and anchored sheet piles. Each 1.0-foot high 41 drop will extend across the main channel and key into the overbanks to protect against
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-53 – October 2012 San Joaquin River Restoration Program
1 flanking. Revetment is included along both channel banks within the portion of the 2 bypass containing the grade control structures to provide additional protection against 3 flanking. It is assumed that the revetment will consist of buried riprap covered with 4 topsoil, erosion control fabric, and native vegetation.
5 7.3.10 Fresno Slough Dam 6 The Fresno Slough Dam will be constructed approximately 0.5 miles south of the 7 Mendota Dam, in the existing Fresno Slough. In addition, the dam structure will be 8 located just south of the existing Mowry Bridge that crosses the Fresno Slough. The dam 9 will serve to limit the extent of Mendota Pool so it no longer occupies portions of the San 10 Joaquin River. This pool will feed the five existing irrigation canals (Main Canal, Helm 11 Ditch, Columbia Canal, Outside Canal, and Main Lift Canal). A screened water diversion 12 canal would enable water deliveries from the San Joaquin River to the Mendota Pool. 13 Since inputs into the Mendota Pool will be screened, Fresno Slough Dam does not 14 require provisions for fish passage.
15 The dam structure was preliminarily designed to accommodate a maximum water 16 elevation of 156.0 feet. This water elevation corresponds to a pool depth of 16.0 feet 17 above the top of the concrete floor.
18 The Fresno Slough Dam consists of a reinforced concrete spillway with a top elevation of 19 140.0 feet. The spillway does not require the support of piles. The spillway includes a 20 concrete cutoff wall at the upstream end of the spillway to limit the hydrostatic uplift 21 pressures and reduces the effects of scour. Baffle blocks and riprap are included at the 22 downstream end of the concrete spillway to limit the effects of scour and erosion.
23 Directly adjacent to the upstream and downstream ends of the concrete dam structure, a 24 total of four concrete retaining walls form the walls of the spillway, and retain the sides 25 of the earthen embankment portion of the dam. The spillway structure is comprised of 26 multiple gates, which serve to control the flow of water from the Mendota Pool to the San 27 Joaquin River.
28 Over the dam, a concrete roadway, concrete maintenance platform, and a hoist operation 29 platform span the full width of the structure. A series of vertical stoplog slots would be 30 included in the concrete abutment walls. The stoplog slots allow the placement of 31 stoplogs directly upstream of the gates, to facilitate local dewatering of the gates for 32 maintenance operations.
33 Some excavation of existing channel sediments upstream of the dam will be required to 34 improve flow conditions through the dam during Kings River floods.
35 7.3.11 Mendota Dam Fish Passage Facilities
36 Boards-Out Conditions 37 For the Fresno Slough Dam, two sharp crested weirs downstream of Mendota Dam will 38 increase the water surface elevation during low flows around 100 cfs to allow fish 39 passage over the top of sill when the boards are out at Mendota Dam. The weirs are
Mendota Pool Bypass and Reach 2B Improvements Project 7-54 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 located about 400 feet apart. Each drop structure will raise the water surface about 0.6 2 feet upstream of the structure.
3 The weirs could be formed of vinyl or aluminum sheet piles. The sheet piles will be 4 anchored into earthen layers beyond the channel bed for lateral and foundation support. 5 Riprap will be built along the riverbank upstream and downstream of each of the 6 structures to protect the channel from erosion. It is assumed that the revetment will 7 consist of buried riprap covered with topsoil, erosion control fabric, and native 8 vegetation.
9 Boards-In Conditions 10 For the Short Canal option on the Fresno Slough Dam, the boards at Mendota Dam would 11 be replaced to backwater the Mendota Pool. A proposed fish ladder enables fish to pass 12 over Mendota Dam when the boards are in. The ladder transitions from a minimum San 13 Joaquin River water surface elevation Reach 3 (occurring during low flow/base flow 14 conditions) to the normal pool water surface elevation above Mendota Dam. Design of 15 the ladder follows the general guidelines in the Anadromous Salmonid Passage Facility 16 Design (NMFS 2008). A vertical slot configuration was selected because this 17 configuration has been used successfully to facilitate the upstream migration of salmon 18 and steelhead (NMFS 2008).
19 The design of the fish ladder is the same as that presented for the Chowchilla Bifurcation 20 Structure retrofit in Section 7.3.1.
21 7.3.12 Main Canal and Helm Ditch Relocations 22 The Fresno Slough Dam requires the headworks of the Central California Irrigation 23 District’s (CCID) Main Canal and Helm Ditch to be reconfigured to divert water from the 24 upstream (south) side of the Fresno Slough Dam. This will allow the District to continue 25 to receive their water supply from the Delta Mendota Canal and flows from the Fresno 26 Slough without requiring screening of those diversions.
27 To provide water to the CCID’s Main Canal and Helm Ditch, an inlet canal is proposed 28 that will take water from the upstream side of the proposed Fresno Slough Dam, run 29 north adjacent to the west side of the San Joaquin River, and connect to the Main Canal 30 and Helm Ditch just west of their current intakes. This canal will be capable of conveying 31 the full flow of both the Main Canal and the Helm Ditch combined (1550 cfs).
32 The inlet canal would be designed to pass the design flow at anticipated low water levels 33 in the Pool, but it would still provide 2 feet of freeboard at the anticipated high water 34 level. The water elevation in the inlet canal would essentially float with the Mendota 35 Pool. A bridge over the inlet canal would be required to maintain access to Mowry 36 Bridge and the future Fresno Slough Dam. Currently, there is a 20-inch drinking water 37 pipeline for the City of Mendota that crosses the Mowry Bridge. This pipeline would 38 need to be modified so that it crosses the proposed inlet canal on the proposed bridge.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-55 – October 2012 San Joaquin River Restoration Program
1 The inlet canal would be concrete lined in locations where erosion is likely to be a 2 concern (i.e., at bends and transitions), and riprap would be placed at the transition from 3 the Pool to the inlet channel.
4 A concrete control structure would control the water from the inlet canal. It would 5 function to control flows to both the Main Canal and the Helm Ditch. Controlling the 6 flow to the Main Canal would be accomplished with control gates Upstream of the gates 7 on the eastern wall, a pipeline would deliver water to the relocated head of the Helm 8 Ditch. The concrete pipe, equipped with a canal gate, would serve to control the flow rate 9 as well as shutoff point. It is assumed that existing headworks and telemetry for both the 10 Main Canal and Helm Ditch would be removed from the site, and new telemetry would 11 be installed.
12 The upstream side of the Main Canal structure would have a cutoff wall to prevent 13 undermining the structure. Downstream of the control structure, the Main Canal would 14 transition both vertically and horizontally into the existing Main Canal alignment and 15 cross-section. The extension of Helm Ditch would be designed to match the cross-section 16 of the existing Helm Ditch downstream.
17 7.4 Project Options
18 7.4.1 Bend 10 Revetment or Columbia Canal Relocation 19 At Bend 10 (approximately RM 209), the channel runs along the right-bank levee, and 20 the Columbia Canal is located adjacent on the north side of the levee. For the Floodplain 21 Initial Alternatives, levee alignments were typically placed with a minimum 300-foot 22 buffer between the channel and the levee. Due to the proximity, the portion of the 23 Columbia Canal along Bend 10 would need to be relocated in order to accommodate the 24 300-foot buffer. If the Columbia Canal is not relocated and the buffer is not included, the 25 levee will require revetment to protect it from erosion. To examine the range of benefits 26 and impacts, the revetment and the Columbia Canal relocation were both analyzed as 27 project options. Either option can be combined with the Floodplain Initial Alternatives.
28 The revetment design assumes an average waterside slope of 1.5H to 1V, average riprap 29 thickness of 3 feet, a 6-foot riparian bench, 1-foot of rock slope protection and 7.5 feet of 30 launch rock (the rock placed along the bank below the mean water surface elevation).
31 Land Acquisition 32 Approximately 18 acres of additional lands will need to be acquired to accommodate the 33 Columbia Canal relocation. No additional lands are required for the revetment option.
Mendota Pool Bypass and Reach 2B Improvements Project 7-56 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1
2 Figure 7-6. 3 Bend 10 Levee Alignment
4 Table 7-33. 5 Bend 10 Options Revetment Columbia Canal Relocation Revetment/Levee Length 2,752 feet 2,934 feet Canal Relocations - 2,500 feet Pump Relocations 2 2 Land Acquisition - 18 acres 6
7 7.4.2 Water Delivery Canal Options 8 The Fresno Slough Dam includes three optional canals for delivering up to 2,500 cfs in 9 water deliveries from the San Joaquin River into Mendota Pool: North Canal, South 10 Canal, and Short Canal. The North and South Canal alignments connect to the river at 11 approximately RM 214.2, upstream of San Mateo Avenue, and discharge water to Fresno 12 Slough at locations approximately 1.8 and 2.3 river miles south of Mendota Dam, 13 respectively. The South Canal discharges via the Little San Joaquin Slough. The Short 14 Canal option would be located directly east of the Fresno Slough Dam. Any of the 15 options can be combined with the Fresno Slough Dam.
16 In addition, the North and South canals could be combined with the Settlement and 17 Compact alignments; in this case the water diversion point would be relocated from the 18 head of the bypass channel to the head of the water delivery canal.
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1 North and South Canals 2 Water deliveries would be controlled at the upstream ends of the North and South canals 3 by a bifurcation structure of similar design to those used for the Settlement and Compact 4 alignments. The river control structure would have a fish ladder for fish passage, and the 5 canal control structure would have a fish screen to prevent entrainment. The control 6 structures, fish screen, and fish ladders are discussed in Section 7.3.
7 The North and South canals can be concrete-lined or unlined. The current unlined design 8 assumes maintained grasses. All canals will have a trapezoidal cross-section. The lined 9 North and South canals have a top-width of approximately 88 feet, a total corridor width 10 of approximately 175 feet (including levees and maintenance roads), and 2H to 1V side 11 slopes on the canal and levees. The unlined North and South canals have top-widths of 12 approximately 235 and 270 feet, respectively, total corridor widths of approximately 435 13 and 490 feet (including levees and maintenance roads), respectively, and 3H to 1V side 14 slopes on the canal and levees.
15 Levee heights are based on a flow of 2,500 cfs and three feet of freeboard. Seepage 16 control measures and erosion protection would be included as necessary to minimize 17 seepage impacts and reduce erosion and scour in the canal. However, seepage is assumed 18 not be an issue for a lined canal, so seepage control measures would be not provided for 19 the lined canal.
20 The North and South canals will cross San Mateo Avenue, so bridge crossings are 21 assumed. The costs include a concrete deck, reinforcing steel, piles, and pile extensions, 22 railing, excavation, and backfill; however, design details are yet to be refined.
23 Current costs are based on the assumptions that suitable earthen fill materials will be 24 available within 1 mile of the levee locations and that some modification to soils will be 25 required to meet permeability requirements. Once the borrow source for the levees is 26 identified, import and hauling costs may be updated.
27 Short Canal 28 For the Short Canal, Mendota Dam will function as the river control structure during 29 water deliveries to the Pool, so only the canal control structure will be constructed. Here, 30 Mendota Dam will be equipped with fish passage facilities, and again, the canal control 31 structure will have a fish screen. The control structures, fish screen, and fish ladders are 32 discussed in Section 7.3.
33 The Short Canal would deliver up to 2,500 cfs in water deliveries from the San Joaquin 34 River to Mendota Pool. The Short Canal would discharge into Fresno Slough 35 approximately 0.8 river miles south of Mendota Dam.
36 The Short Canal would be concrete-lined with a trapezoidal cross-section. The Short 37 Canal would have a top-width of approximately 70 feet, a total corridor width of 38 approximately 180 feet (including levees and maintenance roads), and 2H to 1V side 39 slopes on the canal banks and 3H to 1V side slopes on the levees. Levee heights would 40 be based on a flow of 2,500 cfs and two feet of freeboard.
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1 Land Acquisition 2 Approximately 82, 205, 82, 199, and 8 acres of additional lands will need to be acquired 3 to accommodate the North Canal (lined and unlined), South Canal (lined and unlined), 4 and Short Canal, respectively.
5 Construction Considerations 6 Construction of the North and South canals will need to be coordinated with construction 7 of the Floodplain Initial Alternatives levees because depending on the alternative, levees 8 may be shared.
9 Construction of the fish screen and return/bypass fish pipes will take place in the dry 10 using conventional construction methods and must be coordinated with construction of 11 the water delivery canal. The exception to this is the outlet for the fish return pipes, which 12 will require a cofferdam. All fish facility structures and pipes with surfaces exposed to 13 fish require additional attention to surface-smoothness.
14 For construction of the control structures and fish ladders, a minimum flow must be 15 maintained during construction; the amount or range of flows has not yet been identified. 16 For construction at the bifurcation, it was assumed that construction would first be done 17 away from the fish ladder. A sheet pile cofferdam would be provided for the river control 18 structure and/or the canal control structure and the water diverted away from the 19 construction. Additional sheet piling will be provided to divert flows through the new 20 bifurcation structure while the fish ladder is constructed.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 7-59 – October 2012 San Joaquin River Restoration Program
1 Table 7-34. 2 Fresno Slough Dam Levees, Relocations, and Land Acquisition Left Levee Right Levee Levee Length North Canal (lined and unlined) 4.0 miles 4.0 miles South Canal (lined and unlined) 3.3 miles 3.3 miles Short Canal 0.2 miles 0.2 miles Average Levee Height North Canal (lined) 3.9 feet 3.9 feet North Canal (unlined) 3.0 feet 3.0 feet South Canal (lined) 4.3 feet 4.3 feet South Canal (unlined) 3.1 feet 3.1 feet Short Canal 6.3 feet 6.3 feet Fill Volume North Canal (lined) 147,800 cubic yards 147,800 cubic yards North Canal (unlined) 140,700 cubic yards 140,700 cubic yards South Canal (lined) 154,900 cubic yards 154,900 cubic yards South Canal (unlined) 109,900 cubic yards 109,900 cubic yards Short Canal 8,800 cubic yards 8,800 cubic yards Relocations 6,300 feet (North Canal) Electrical Distribution Facility - 4,000 feet (South Canal) 1,100 feet (North Canal) Gas Transmission Groundwater Well 2 (North & South canals) 500 feet (South Canal) 3,800 feet (North Canal) Water Pipeline Lift Pump 2 (South Canal) 1,400 feet (South Canal) 11,900 feet (North Canal) Canal Power Pole - 4,300 feet (South Canal) Confluence - Monitoring Well - Culvert - Regulating Reservoir - Diversion - Abandoned Well - 1,200 ft2 (North Canal) Barn/Shed 2,200 ft2 (South Canal) Land Acquisition1 82 acres (North Canal lined), 205 acres (North Canal unlined) Total 82 acres (South Canal lined), 199 acres(South Canal unlined) 8 acres (Short Canal) 3 1 Land acquisition total includes areas that may be State of California sovereign lands or public trust lands. 4
5 7.4.3 7,000 cfs Capacity 6 Floodplain and Bypass Initial Alternatives were designed for conveyance of up to 4,500 7 cfs in Restoration Flows from Reach 2A downstream to Reach 3 and diversion of up to 8 2,500 cfs to Mendota Pool. In order to make irrigation deliveries, Restoration Flows over 9 2,000 cfs may be reduced because the total flow is capped at the 4,500 cfs capacity. The 10 7,000 cfs capacity option can be included with any of the Final Alternatives.
11 If the SJRRP wants to convey Restoration Flows up to 4,500 cfs while simultaneously 12 making irrigation deliveries up to 2,500 cfs to the Pool, the capacity in Reach 2B at some
Mendota Pool Bypass and Reach 2B Improvements Project 7-60 – October 2012 Attachment A – Initial Alternatives Evaluation 7.0 Initial Alternatives Descriptions
1 locations would need to be increased to 7,000 cfs. This will require modifications to the 2 appraisal-level designs and costs for the levees, structures, and other elements. The total 3 length of the Project that will need to convey 7,000 cfs depends on the Bypass Initial 4 Alternative. For the Settlement Alignment, 8 river miles of the Project would need to 5 handle 7,000 cfs. For the Compact Alignment, it is 10 river miles. For the Fresno 6 Slough Dam with the North or South canal, only 2 river miles would need to handle 7 7,000 cfs, but for the Fresno Slough Dam with the Short Canal, it is 10.5 river miles.
8
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1 8.0 Initial Alternatives Evaluation Results 2 Results of the alternatives evaluation can be found summarized in the evaluation matrix 3 and supporting data provided in Attachment B. The evaluation matrix is structured such 4 that evaluation criteria are grouped into factors, factors are grouped into categories, and 5 categories are grouped into perspectives. Each alternative’s score is also grouped at these 6 levels so that the interplay between various resource areas and perspectives can be better 7 understood. The discussion in this chapter refers to the various levels of the evaluation, 8 and it is useful to refer to the matrix while reading these sections. A summary of the 9 results of the evaluation is provided in Figure 8-1; higher bars indicate higher scores and 10 more preferable alternatives.
11
12 Figure 8-1 13 Summary of Evaluation Results
14 8.1 Evaluation by Settlement Goals and Settlement Defined 15 Improvements
16 The initial guidance used in the development of the Project came from language in the 17 Settlement, specifically the Settlement’s goals and the defined improvements. The 18 Settlement goals are:
19 The Restoration Goal (Settlement Paragraph 2):
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 8-1 – October 2012 San Joaquin River Restoration Program
1 … a goal of this Settlement is to restore and maintain fish populations 2 in “good condition” in the main stem of the San Joaquin River below 3 Friant Dam to the confluence of the Merced River, including 4 naturally-reproducing and self-sustaining populations of salmon and 5 other fish (the “Restoration Goal”).
6 The Water Management Goal (Settlement Paragraph 2):
7 …a goal of this Settlement is to reduce or avoid adverse water supply 8 impacts to all of the Friant Division long-term contractors that may 9 result from the Interim Flows and Restoration Flows provided for in 10 this Settlement (the “Water Management Goal”).
11 The Mendota Pool Bypass and Reach 2B improvements defined in the Settlement are 12 (Settlement Paragraph 11(a)):
13 (1) Creation of a bypass channel around Mendota Pool to ensure 14 conveyance of at least 4,500 cfs from Reach 2B downstream to Reach 15 3. This improvement requires construction of a structure capable of 16 directing flow down the bypass and allowing the Secretary to make 17 deliveries of San Joaquin River water into Mendota Pool when 18 necessary;
19 (2) Modifications in channel capacity (incorporating new floodplain 20 and related riparian habitat) to ensure conveyance of at least 4,500 cfs 21 in Reach 2B between the Chowchilla Bifurcation Structure and the 22 new Mendota Pool bypass channel.
23 The Initial Alternatives are designed such that one Floodplain Initial Alternative is paired 24 with one Bypass Initial Alternative to create a complete Project Alternative. All paired 25 combinations of the Initial Alternatives will work towards meeting the Settlement 26 Restoration Goal by providing suitable passage conditions for adult and juvenile 27 salmonids and transient rearing habitat for juvenile salmonids, two key components for 28 supporting a fish population in “good condition” (SJRRP 2010c). The Project has limited 29 to no effect on meeting the Water Management Goal.
30 All paired combinations of the Initial Alternatives meet the requirements of the project- 31 specific improvements in Settlement Paragraphs 11(a)(1) and 11(a)(2) by:
32 • Bypassing the Mendota Pool 33 • Designing for conveyance of at least 4,500 cfs in the Mendota Pool Bypass 34 • Designing in-channel and levee structures that allow the Secretary to make 35 deliveries of San Joaquin River water into Mendota Pool when necessary 36 • Designing for channel and floodplain capacity of at least 4,500 cfs in Reach 2B 37 between the Chowchilla Bifurcation Structure and the new Mendota Pool bypass 38 channel
Mendota Pool Bypass and Reach 2B Improvements Project 8-2 – October 2012 Attachment A – Initial Alternatives Evaluation 8.0 Initial Alternatives Evaluation Results
1 • Incorporating new floodplain and related riparian habitat between the Chowchilla 2 Bifurcation Structure and the new Mendota Pool bypass channel
3 8.2 Evaluation by Initial Alternative
4 The sections below discuss the results of the alternatives evaluation for each Initial 5 Alternative.
6 8.2.1 FP-1 7 FP-1 has relatively the lowest cost, particularly land costs and restoration costs, and one 8 of the shortest construction timelines. FP-1 provides the least amount of floodplain and 9 the least amount of rearing habitat of all the alternatives. The limited floodplain width 10 results in low acreages of very shallow water habitat and may not provide sufficient 11 levels of productivity. There are no up or downstream fish passage issues associated with 12 this alternative. FP-1 has the least amount of restoration area for vegetation and wildlife 13 and is more likely to have channel stability issues. FP-1 has the most acreage of potential 14 nuisance seepage because the relatively narrower floodplain results in greater water 15 depths and increased hydraulic gradients through the levees. FP-1 requires the least 16 amount of land to be removed from production. FP-1 has relatively slightly more 17 environmental impacts due to proposed levees impacting more existing habitat because 18 they are located nearer the river channel, resulting in a longer overall levee length.
19 8.2.2 FP-2 20 FP-2 has relatively moderate costs, particularly capital improvement costs, and one of the 21 shortest construction timelines. FP-2 provides a moderate amount of floodplain habitat 22 resulting in sufficient acres of the very shallow water habitat for primary production as 23 well as sufficient acres of habitat that supporting direct rearing. There are no up or 24 downstream fish passage issues associated with this alternative. FP-2 has relatively 25 moderate amounts of restoration area for vegetation and wildlife and is equally likely to 26 have channel stability issues as not. FP-2 has relatively moderate acreage of potential 27 nuisance seepage. FP-2 requires relatively moderate amounts of land to be removed from 28 production. FP-2 has relatively moderate environmental impacts.
29 8.2.3 FP-3 30 FP-3 has relatively moderate costs and one of the shortest construction timelines. FP-3 31 provides a moderate amount of floodplain habitat resulting in sufficient acres of shallow 32 water habitat for primary production as well as sufficient acres of habitat supporting 33 direct rearing. In addition, grading areas for this alternative increase the amount of 34 floodplain habitat available at lower flows. There are no up or downstream fish passage 35 issues associated with this alternative. FP-3 has relatively moderate amounts of 36 restoration area for vegetation and wildlife and is equally likely to have channel stability 37 issues as not. FP-3 has relatively moderate acreage of potential nuisance seepage. FP-3 38 requires relatively moderate amounts of land to be removed from production. FP-3 has 39 relatively slightly more environmental impacts due to the grading area impacting existing 40 habitats.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 8-3 – October 2012 San Joaquin River Restoration Program
1 8.2.4 FP-4 2 FP-4 has relatively somewhat higher costs and somewhat longer construction timelines. 3 FP-4 provides sufficient rearing habitat on the floodplain, but at flows of around 2,000 to 4 2,500 cfs, there are about equal acres of shallow water habitat and direct rearing habitat, 5 and about half of the shallow water habitat is less than 0.5 feet deep. This results in fair 6 quality shallow water habitat. There are no up or downstream fish passage issues 7 associated with this alternative. FP-4 has relatively greater amounts of restoration area 8 for vegetation and wildlife and is relatively somewhat less likely to have channel stability 9 issues. FP-4 has relatively lower acreage of potential nuisance seepage. FP-4 requires 10 relatively higher amounts of land to be removed from production. FP-4 has relatively 11 moderate environmental impacts.
12 8.2.5 FP-5 13 FP-5 has relatively the highest costs and longest construction timelines. FP-5 provides 14 more shallow water habitat than direct rearing habitat at flows of about 2,500 cfs, and 15 about half of the shallow water habitat is less than 0.5 feet deep. There are no up or 16 downstream fish passage issues associated with this alternative. FP-5 has the greatest 17 amounts of restoration area for vegetation and wildlife and is relatively the least likely to 18 have channel stability issues. FP-5 has relatively the least acreage of potential nuisance 19 seepage because the relatively wider floodplain results in lowest water depths and 20 decreased hydraulic gradients through the levees. FP-5 requires relatively the most 21 amount of land to be removed from production. FP-5 has relatively moderate 22 environmental impacts.
23 8.2.6 Settlement Alignment 24 Compared to the other Bypass Initial Alternatives, the Settlement Alignment has 25 relatively moderate costs and construction timelines. The Settlement Alignment has 26 relatively fewer fish habitat and passage benefits including minimal additional shallow 27 water or rearing habitat and relatively more structures, steps, and potential predation 28 sites. The Settlement Alignment has the least amounts of restoration area for vegetation 29 and wildlife and is relatively the most likely to have channel stability issues both because 30 it shortens the overall length of the river. The Settlement Alignment requires relatively 31 the most amount of land to be removed from production. The Settlement Alignment has 32 relatively the least environmental impacts.
33 8.2.7 Compact Alignment 34 Compared to the other Bypass Initial Alternatives, the Compact Alignment has relatively 35 the lowest costs, particularly land costs, and relatively moderate construction timelines. 36 The Compact Alignment has relatively fewer fish habitat and passage benefits including 37 minimal additional shallow water, a reduction in overall rearing habitat, and relatively 38 more structures, steps, and potential predation sites. The Compact Alignment has 39 relatively moderate amounts of restoration area for vegetation and wildlife and is equally 40 likely to have channel stability issues as not. The Compact Alignment requires relatively 41 the least amount of land to be removed from production. The Compact Alignment has 42 relatively moderate environmental impacts.
Mendota Pool Bypass and Reach 2B Improvements Project 8-4 – October 2012 Attachment A – Initial Alternatives Evaluation 8.0 Initial Alternatives Evaluation Results
1 8.2.8 Fresno Slough Dam 2 Compared to the other Bypass Initial Alternatives, the Fresno Slough Dam has relatively 3 the highest costs, particularly capital improvement costs, and relatively longer 4 construction timelines. Fresno Slough Dam has relatively greater fish habitat and 5 passage benefits including additional rearing habitat and relatively fewer structures, steps, 6 and potential predation sites. Fresno Slough Dam has relatively moderate amounts of 7 restoration area for vegetation and wildlife and is least likely to have channel stability 8 issues. Fresno Slough Dam requires relatively moderate amounts of land to be removed 9 from production. Fresno Slough Dam has relatively the most environmental impacts.
10 8.3 Comparisons of Initial Alternatives
11 The following sections provide comparative discussions of the Initial Alternatives for 12 selected criteria, the three perspective levels, and overall.
13 8.3.1 Based on Fish Habitat and Passage Criteria 14 In the evaluation of Initial Alternatives based on fish habitat and passage, FP-2 and FP-3 15 score the best and FP-1 scores the worst, but FP-4 and FP-5 score nearly as well as FP-2 16 and FP-3 (see Table 8-1). This is primarily related to the relative amounts of the shallow 17 water habitat in each Floodplain Initial Alternative. FP-2 and FP-3 have the best ratings 18 for proportion of very shallow water habitat relative to rearing habitat, and FP-1 and FP-5 19 have the worst ratings. This is because FP-1 has very limited areas shallow water habitat 20 and FP-5 is so wide that a large proportion of the floodplain is very shallow. FP-2 and 21 FP-3 have the same floodplain width, with FP-3 providing some additional inundation at 22 moderate flows from grading the floodplain. FP-4 functions intermediate to FP-2/FP-3, 23 and FP-5 but large areas of shallow water occur at modeled flows of 2,500 cfs. In 24 combination with the extensive shallow water at the inundation Index Flow and the much 25 higher potential for fish stranding, FP-5 does not function for fish as well as FP-2, FP-3, 26 or FP-4. The Floodplain Initial Alternatives perform equivalently under the passage 27 criteria.
28 For the Bypass Initial Alternatives, Fresno Slough Dam scores the best and the 29 Settlement and Compact alignments score equally and less than the Fresno Slough Dam. 30 Fresno Slough Dam has a number of criteria contributing to its higher score, including: 31 the higher amount of rearing habitat and the fewer number of structures, steps, and 32 potential predation sites. While the Settlement Alignment provides no additional 33 shallow water or rearing habitat, the Compact Alignment lowers the water level upstream 34 thus reducing the quantity of rearing habitat in the Floodplain Initial Alternatives. The 35 Settlement and Compact alignments perform equivalently under the passage criteria.
36 For the project options, the objectives and benefits achievement criteria do not apply to 37 the Bend 10 options. While the Short Canal scores the best of the water delivery canals 38 for Fresno Slough Dam, and the remaining options score equivalently.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 8-5 – October 2012 San Joaquin River Restoration Program
1 Table 8-1. 2 Initial Alternative Rankings for Fish Habitat and Passage Criteria Floodplain Bypass Bend 10 Options Water Delivery Rank Alternative Alternative Canal Options
1st FP-2 and FP-3 Fresno Slough Dam n/a Short Canal Lined North Canal, nd Settlement Alignment Unlined North Canal, 2 Compact Alignment Lined South Canal, Unlined South Canal 3rd FP-4
4th FP-5
5th FP-1
3
4 8.3.2 Based on Costs 5 In the evaluation of Initial Alternatives based on costs, three separate cost items (capital 6 improvements, land, and operation and maintenance (O&M) costs) were analyzed. For 7 the Floodplain Initial Alternatives, FP-1, FP-2, and FP-3 score similarly well in all three 8 costs criteria (see Table 8-2). FP-2 has the lowest capital improvement costs, FP-1 the 9 lowest land and O&M costs. FP-5 costs are highest of the Floodplain Initial Alternatives 10 for all three costs criteria. This is strongly influenced by the amount of restoration area in 11 each Floodplain Initial Alternative and the cost of planting. FP-4 and FP-5 are the 12 cheapest to construct infrastructure-wise, but the revegetation costs out-weigh this and 13 result in higher overall costs. Likewise, FP-1 is the most expensive to construct 14 infrastructure-wise, but it has the least revegetation costs and results in a cheaper overall 15 alternative.
16 For the Bypass Initial Alternatives, the Settlement Alignment has the lowest capital 17 improvement costs, while the Compact Alignment’s capital improvement costs are 18 similar but slightly more. The Compact Alignment has the lowest land costs, and the 19 Settlement Alignment has the lowest O&M costs.
20 For the project options, the Bend 10 levee revetment is significantly more expensive than 21 the Columbia Canal Relocation. The Short Canal is the least expensive water delivery 22 canal option for the Fresno Slough Dam. If an alternative diversion point for the 23 Settlement or Compact alignments is desired, then lined South Canal would be the least 24 expensive option.
Mendota Pool Bypass and Reach 2B Improvements Project 8-6 – October 2012 Attachment A – Initial Alternatives Evaluation 8.0 Initial Alternatives Evaluation Results
1 Table 8-2. 2 Initial Alternative Rankings for Costs Criteria Floodplain Bypass Bend 10 Options Water Delivery Rank Alternative Alternative Canal Options
1st FP-1 Compact Alignment Levee Revetment Short Canal
nd Columbia Canal 2 FP-2 and FP-3 Settlement Alignment Lined South Canal Relocation 3rd Fresno Slough Dam Lined North Canal
4th FP-4 Unlined South Canal
5th FP-5 Unlined North Canal
3
4 8.3.3 Based on Implementation/Technical Feasibility Perspective 5 The evaluation of the Initial Alternatives at the implementation and technical feasibility 6 perspective is similar to the discussion in Section 8.3.2 for costs with the addition of 7 construction timeline being considered.
8 For the Floodplain Initial Alternatives, FP-1 scores the best and FP-5 scores the worst at 9 this perspective level, but FP-2 and FP-3 score nearly as well as FP-1 (see Table 8-3). 10 This is strongly influenced by the amount of restoration area in each Floodplain Initial 11 Alternative and the cost of planting. FP-4 and FP-5 are the cheapest to construct 12 infrastructure-wise, but the revegetation costs out-weigh this and result in higher overall 13 costs. Conversely, FP-1 is the most expensive to construct infrastructure-wise, but it has 14 the least revegetation costs and results in a cheaper overall alternative.
15 For the Bypass Initial Alternatives, the Compact Alignment scores the best and Fresno 16 Slough Dam scores the worst. For the project options, the Bend 10 levee revetment 17 scores the better, and the Short Canal scores the best of the water delivery canals for 18 Fresno Slough Dam. If an alternative diversion point for the Settlement or Compact 19 alignments is desired, then the lined South Canal scores the best of the available options.
20 Table 8-3. 21 Initial Alternative Rankings for Implementation/Technical Feasibility Perspective Floodplain Bypass Bend 10 Options Water Delivery Rank Alternative Alternative Canal Options
1st FP-1 Compact Alignment Levee Revetment Short Canal
nd Columbia Canal 2 FP-2 and FP-3 Settlement Alignment Lined South Canal Relocation 3rd Fresno Slough Dam Lined North Canal
4th FP-4 Unlined South Canal
5th FP-5 Unlined North Canal
22
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 8-7 – October 2012 San Joaquin River Restoration Program
1 8.3.4 Based on Objectives/Benefits Achievement Perspective 2 Under the evaluation of the Initial Alternatives at the objectives and benefits achievement 3 perspective for the Floodplain Initial Alternatives, FP-5 scores the best and FP-1 scores 4 the worst, but FP-4 scores nearly as well as FP-5 (see Table 8-4). This is primarily 5 related to the amount of restoration area (vegetation and wildlife) in each Floodplain 6 Initial Alternative. FP-4 and FP-5 have the most restoration area thus providing the most 7 overall benefits. Conversely, FP-1 has the least restoration area and thus provides the 8 least overall benefits. Additionally, the wider floodplain with FP-4 and FP-5 9 significantly reduces the risk of channel instability thus contributing to the benefits of 10 these Initial Alternatives, while FP-1 is more likely to have channel stability issues, 11 which reduces the relative benefits.
12 For the Bypass Initial Alternatives, Fresno Slough Dam scores the best and the 13 Settlement Alignment scores the worst. This is primarily related to the amount of 14 restoration area and the length of the river channel. The restoration area for the 15 Settlement Alignment is limited to the bypass channel corridor, which also shortens the 16 river’s length, so it has relatively smaller restoration area and less benefits. While Fresno 17 Slough Dam has the longest river length and incorporates floodplain habitat along that 18 length, providing more restoration area and greater benefits.
19 For the project options, the objectives and benefits achievement criteria do not apply to 20 the Bend 10 options. While the Short Canal scores the best of the water delivery canals 21 for Fresno Slough Dam, and the remaining options score equivalently.
22 Table 8-4. 23 Initial Alternative Rankings for Objectives/Benefits Achievement Perspective Floodplain Bypass Bend 10 Options Water Delivery Rank Alternative Alternative Canal Options
1st FP-5 Fresno Slough Dam n/a Short Canal Lined North Canal, nd Unlined North Canal, 2 FP-4 Compact Alignment Lined South Canal, Unlined South Canal 3rd FP-2 and FP-3 Settlement Alignment
4th
5th FP-1
24
25 8.3.5 Based on Impacts Perspective 26 Under the evaluation of the Initial Alternatives at the impacts perspective for the 27 Floodplain Initial Alternatives, FP-1 scores the best and FP-5 scores the worst, but FP-2 28 and FP-3 score nearly as well as FP-1 (see Table 8-5). This is primarily related to the 29 amount of land required by each Floodplain Initial Alternative. FP-5 has the largest area 30 and takes the most land of the Initial Alternatives thus causing the largest impact to
Mendota Pool Bypass and Reach 2B Improvements Project 8-8 – October 2012 Attachment A – Initial Alternatives Evaluation 8.0 Initial Alternatives Evaluation Results
1 agriculture and land use. Conversely, FP-1 has the smallest area, takes the least amount 2 of land of the Initial Alternatives, and causes less impact to agriculture.
3 For the Bypass Initial Alternatives, the Compact Alignment scores the best and the 4 Settlement Alignment scores the worst. This is primarily related to the amount of land 5 required by each Bypass Initial Alternative. The Settlement Alignment results in 6 additional land outside the bypass channel corridor being inaccessible or unusable for 7 agricultural purposes, so it has the largest land acquisition area and takes the most land of 8 the Initial Alternatives thus causing more impacts to agriculture and land use. 9 Conversely, the Compact Alignment has the smallest area, takes the least amount of land 10 of the Initial Alternatives, and causes less impact to agriculture.
11 For the project options, the Bend 10 levee revetment scores the better because it does not 12 require additional land. The Short Canal scores the best of the water delivery canals for 13 Fresno Slough Dam. If an alternative diversion point for the Settlement or Compact 14 alignments is desired, then the lined South Canal scores the best of the available options.
15 Table 8-5. 16 Initial Alternative Rankings for Impacts Perspective Floodplain Bypass Bend 10 Options Water Delivery Rank Alternative Alternative Canal Options
1st FP-1 Compact Alignment Levee Revetment Short Canal
nd Columbia Canal 2 FP-2 and FP-3 Fresno Slough Dam Lined South Canal Relocation 3rd Settlement Alignment Lined North Canal
4th FP-4 Unlined North Canal
5th FP-5 Unlined South Canal
17
18 8.3.6 Based on All Criteria 19 Comparisons of the Initial Alternatives based on all the criteria can be viewed by looking 20 at the total score at each of the four evaluation levels (criteria, factor, category, and 21 perspective). Essentially, the perspectives have equal weight in the total or overall score 22 at the perspective level, the categories have equal weight in the total or overall score at 23 the category level, the factors have equal weight in the total or overall score at the factor 24 level, and the criteria have equal weight in the total or overall score at the criteria level.
25 FP-2, FP-3, and FP-4 rank at the top at the factor, category, and perspective levels, and 26 FP-1 consistently ranks at or near the bottom. FP-5 ranks at or near the bottom at all but 27 the criteria level, where it ranks first. The Compact Alignment, Fresno Slough Dam, and 28 the Settlement Alignment consistently rank first, second, and third, respectively. Table 29 8-6 shows the resulting rankings of the Initial Alternatives according to their total scores.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 8-9 – October 2012 San Joaquin River Restoration Program
1 Table 8-6. 2 Overall Initial Alternative Rankings Perspective Level Category Level
Floodplain Bypass Floodplain Bypass Alternative Rank Alternative Alternative Alternative
1st FP-2 Compact Alignment FP-2 Compact Alignment
2nd FP-3 Fresno Slough Dam FP-3 Fresno Slough Dam
3rd FP-4 Settlement Alignment FP-4 Settlement Alignment
4th FP-1 FP-1
5th FP-5 FP-5
Factor Level Criteria Level
Floodplain Bypass Floodplain Bypass Alternative Rank Alternative Alternative Alternative
1st FP-2 Compact Alignment FP-5 Compact Alignment
2nd FP-3 Fresno Slough Dam FP-4 Fresno Slough Dam
3rd FP-4 Settlement Alignment FP-2 Settlement Alignment
4th FP-5 FP-3
5th FP-1 FP-1 3
4 8.4 Recommended Alternatives for Inclusion in the EIS/R 5 Project Description
6 Two Floodplain Initial Alternatives and two Bypass Initial Alternatives are recommended 7 for inclusion in the Project Description based on their comparatively better performance 8 in the alternatives evaluation. The recommended alternatives are FP-2, FP-4, Compact 9 Alignment, and Fresno Slough Dam.
10 8.4.1 Alternatives Eliminated 11 Three Initial Alternatives are recommended for elimination from consideration based on 12 the evaluation results: FP-1, FP-5, and the Settlement Alignment. These Initial 13 Alternatives are recommended for elimination because they perform relatively poorly 14 when compared to the other Initial Alternatives, or they provide no additional 15 comprehensive benefit with increased cost. The remaining Initial Alternatives (FP-2, FP- 16 3, FP-4, Compact Alignment, and Fresno Slough Dam) provide a better balance between 17 benefits and impacts.
18 FP-1 would result in a confined channel system with high velocities and scour along the 19 corridor requiring expensive bank revetment. Vegetation could be difficult to establish, 20 and water depths would often be too deep to provide effective floodplain rearing and
Mendota Pool Bypass and Reach 2B Improvements Project 8-10 – October 2012 Attachment A – Initial Alternatives Evaluation 8.0 Initial Alternatives Evaluation Results
1 primary production benefits. Based on the results of the evaluation, FP-1 performs poorly 2 for several reasons:
3 • Relatively low amounts of rearing habitat 4 • Poor quality shallow water habitat 5 • Relatively high capital improvement costs 6 • Relatively low amounts of restoration area 7 • Relatively greater risk of channel instability 8 • Relatively larger nuisance seepage impacts 9
10 FP-5 would result in large areas too shallow and dry to provide effective floodplain 11 rearing and primary production benefits. Based on the results of the evaluation, FP-5 12 performs poorly for several reasons:
13 • Poor quality shallow water habitat 14 • Relatively high restoration and land costs 15 • Relatively greater land removed from production 16 • Limited additional fish habitat and passage benefits for the added costs 17 • Potential for fish strandings 18
19 The Settlement Alignment provides less habitat than the Compact Alignment but with 20 higher costs and larger land requirements. Based on the results of the evaluation, the 21 Settlement Alignment performs poorly for several reasons:
22 • Minimal additional shallow water or rearing habitat 23 • Relatively high capital improvement costs 24 • Relatively less restoration area 25 • Relatively greater risk of channel instability 26 • Relatively greater land removed from production 27 In addition, for design and river geometry reasons, a fish barrier at the downstream end of 28 the Settlement Alignment would not be able to meet NMFS criteria. 29 One option is recommended for elimination from consideration based on the evaluation 30 results: Bend 10 Columbia Canal Relocation. This option is recommended for 31 elimination because it performs relatively poorly when compared to the Bend 10 levee 32 revetment, which provides a better balance between benefits and impacts.
33 Based on the results of the evaluation, the Bend 10 Columbia Canal Relocation option 34 performs poorly for several reasons:
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 8-11 – October 2012 San Joaquin River Restoration Program
1 • Additional land acquisition is required 2 • More land removed from production 3 • Relatively greater environmental impacts
4 8.4.2 Alternatives Modified to Reduce Impacts 5 No specific modifications to reduce impacts are recommended at this time but in general, 6 reduction of impacts was a consideration in the concept refinement phase (development 7 of Initial Alternatives). Mitigation measures for avoiding, reducing, compensating for, or 8 minimizing impacts may be developed during the Project EIR/S environmental impact 9 assessments.
10 8.5 Recommended Additional Analysis or Study
11 The items listed below are recommended additional analysis or study of the designs that 12 may be completed if necessary to inform the Project EIS/R assessments.
13 • Selective removal of levees may be refined during the Project EIS/R development 14 to further refine avoidance of existing vegetation and habitat. 15 • Based on input from the TAC regarding the frequency and magnitude of future 16 hydrology in the San Joaquin River system, the quantity and location of 17 floodplain grading may be refined during the Project EIS/R development as an 18 avoidance measure for existing vegetation and habitat and to increase the 19 frequency and acreage of floodplain inundation. However, this must be balanced 20 with the geomorphic analysis concerning channel stability and sediment transport. 21 • Analysis and design of other types of fish ladders or fish ways may be completed 22 to better understand the flows, velocities, depths, and hydraulic jump heights 23 associated with various flow split and delivery operations and whether passage 24 can be further improved and potential predation sites can be reduced. 25 • Analysis and design of other types of fish screens may be completed with the goal 26 of reducing stress on juvenile salmonids, increasing successful downstream 27 migration, or reducing potential predation sites. 28
Mendota Pool Bypass and Reach 2B Improvements Project 8-12 – October 2012 Attachment A – Initial Alternatives Evaluation
1 9.0 Acknowledgments 2 The preparers would like to acknowledge the input and participation of Bureau of 3 Reclamation and other SJRRP staff, third-party consultants, resource agency staff, and 4 others. A partial list of these participants includes:
5 Michelle Banonis Reclamation 6 Lisa Fotherby Reclamation 7 Alicia Gasdick Reclamation 8 Elaina Gordon Reclamation 9 Blair Greimann Reclamation 10 Katrina Harrison Reclamation 11 Jeremy Lorberau Reclamation 12 David Mooney Reclamation 13 Erin Rice Reclamation 14 Karen Dulik DWR 15 David Encinas DWR 16 Greg Farley DWR 17 Alexis Phillips-Dowell DWR 18 Paul Romero DWR 19 Susan Cundiff Tetra Tech 20 Chad Morris Tetra Tech 21 Bob Mussetter Tetra Tech 22 Nick Hindman USFWS 23 Zac Jackson USFWS 24 Becky Lorig USFWS 25 Carl Mesick USFWS 26 Donnie Ratcliff USFWS 27 Stephanie Rickabaugh USFWS 28 Michelle Workman USFWS 29 Larry Brown USGS 30 Steven Phillips USGS 31 George Heise CDFG 32 Dale Stanton CDFG 33 Leslie Mirise NMFS 34 Erin Strange NMFS 35 Steve Thomas NMFS 36
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1 10.0 References 2 Barbour 2007. Barbour, M.G., T. Keeler-Wolf, and A. Schoenherr. Terrestrial 3 Vegetation of California. Third Edition.
4 Byrd 2009. Byrd, B. F., S. Wee, and J. Costello, Far Western Anthropological Research 5 Group, Inc., Davis, California. Cultural Resources Sensitivity Study and Research 6 Design for the San Joaquin River Restoration Program, Fresno, Madera, Merced, 7 and Stanislaus Counties, California. Prepared for U.S. Bureau of Reclamation, 8 Sacramento, California.
9 CDFG 1998. California Department of Fish and Game. California Salmonid Stream 10 Habitat Restoration Manual, Third Edition. January.
11 CDFG 2009. California Department of Fish and Game, Biogeographic Data Branch 12 Vegetation Classification and Mapping Program. List of California Vegetation 13 Alliances. December.
14 CDFG 2010. California Department of Fish and Game. Special Animals (List). 15 Biogeographic Data Branch: California Natural Diversity Database. Updated July 16 2009. Available from web site, http://www.dfg.ca.gov/biogeodata/ 17 cnddb/pdfs/SPAnimals.pdf.
18 Crain 2004. Crain, P.K., K. Whitener, and P.B. Moyle. Use of a Restored Central 19 California Floodplain by Larvae of Native and Alien Fishes. American Fisheries 20 Society Symposium.
21 CVFED 2009. Central Valley Floodplain Evaluation and Delineation and San Joaquin 22 River Restoration Program LiDAR data and aerial imagery. Produced for 23 California Department of Water Resources. April 9.
24 ESRP 2006. Endangered Species Recovery Program, California State University, 25 Stanislaus, Fresno, California. Valley Elderberry Longhorn Beetle Surveys, San 26 Joaquin River, 2004-2005. November 6.
27 Houk 2009. Randy Houk. Personal communication with Susan Hootkins and Duane Paul, 28 ENTRIX. December 9.
29 Jeffres 2008. Jeffres, Carson A., J.J. Opperman and P. B. Moyle. Ephemeral floodplain 30 habitats provide best growth conditions for juvenile Chinook salmon in a 31 California River. Environmental Biology of Fishes. Vol. 83, No. 4. Pages 449- 32 458.
33 NMFS 2001. National Marine Fisheries Service, Southwest Region. Guidelines for 34 Salmonid Passage at Stream Crossings. September.
Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 10-1 – October 2012 San Joaquin River Restoration Program
1 NMFS 2008. National Marine Fisheries Service, Northwest Region. Anadromous 2 Salmonid Passage Facility Design. February. Retrieved from: 3 http://www.nwr.noaa.gov/Salmon- 4 Hydropower/FERC/upload/Fish_Passage_Design.pdf
5 Opperman, 2010. Opperman, J.J., R. Luster, B.A. McKenney, M. Roberts, and A.W. 6 Meadows. Ecological functional floodplains: connectivity, flow regime, and 7 scale. Journal of the American Water Resources Association. April.
8 Pacific States Marine Fisheries Commission 2007. CalFish Passage Assessment 9 Database. Downloaded from www.calfish.org.
10 Reclamation 1967. United States Department of the Interior, Bureau of Reclamation, 11 Central Valley Project, California, Second Amended Contract for Exchange of 12 Waters. Contract I1r-1144, Second Amendatory. September 15, 1967, revised 13 December 6.
14 Reclamation 2006. U.S. Bureau of Reclamation. Water Resources Technical 15 Publication, Fish Protection at Water Diversions, a Guide for Planning and 16 Designing Fish Exclusion Facilities. April.
17 Reclamation Board 1969. Lower San Joaquin River Flood Control Project, Operation 18 and Maintenance Manual for San Joaquin River and Chowchilla Canal Bypass 19 Automatic Control Structures and Appurtenances, Part III.
20 SJRRP 2008. San Joaquin River Restoration Program. Draft Technical Memorandum, 21 Operation Guidelines for Implementing Restoration Flows. April.
22 SJRRP 2010a. San Joaquin River Restoration Program. Draft Daily Flow Time Series. 23 June 16.
24 SJRRP 2010b. San Joaquin River Restoration Program. Draft Mendota Pool Bypass and 25 Reach 2B Improvements Project Technical Memorandum on Environmental Field 26 Survey Results. November.
27 SJRRP 2010c. San Joaquin River Restoration Program. Fisheries Management Plan: A 28 Framework for Adaptive Management in the San Joaquin River Restoration 29 Program. November.
30 SJRRP 2010d. San Joaquin River Restoration Program. Mendota Pool Bypass and Reach 31 2B Improvements Project Public Scoping Report. February.
32 SJRRP 2010e. San Joaquin River Restoration Program. Mendota Pool Bypass and Reach 33 2B Improvements Project Technical Memorandum on Initial Options. April.
34 SJRRP 2010f. San Joaquin River Restoration Program. Mendota Pool Bypass and Reach 35 2B Improvements Project Technical Memorandum on Selection and Use of 36 Analytical Tools. October.
Mendota Pool Bypass and Reach 2B Improvements Project 10-2 – October 2012 Attachment A – Initial Alternatives Evaluation 10.0 References
1 SJRRP 2011a. San Joaquin River Restoration Program. Draft San Joaquin River 2 Restoration Program PEIS/R. April.
3 SJRRP 2011b. San Joaquin River Restoration Program. Draft Seepage Management 4 Plan. March 28.
5 Tetra Tech 2011a. Tetra Tech d.b.a. Mussetter Engineering, Inc. Draft Potential Effects 6 of Eliminating the Mendota Bypass Channel Grade-Control Structures and 7 Mendota Dam. Prepared for California Department of Water Resources. March 8 29.
9 Tetra Tech 2011b. Tetra Tech d.b.a. Mussetter Engineering, Inc. Geomorphic Analysis 10 for the San Joaquin River Reach 2B Alternative Evaluation. Prepared for 11 California Department of Water Resources. January 26.
12 USACE 2000. U.S. Army Corps of Engineers (USACE). Engineer Manual 1110-2-1313 13 Design and Construction of Levees. April 30.
14 USFWS 1996. U.S. Fish and Wildlife Service, Sacramento Fish and Wildlife Service 15 Office, Sacramento, California. Programmatic Formal Endangered Species Act 16 Consultation on Issuance of 404 Permits for Projects with Relatively Small 17 Effects on Listed Vernal Pool Crustaceans Within the Jurisdiction of the 18 Sacramento Field Office, California. February 28.
19 USFWS 2005. U.S. Fish and Wildlife Service, Sacramento Fish and Wildlife Service 20 Office, Sacramento, California. Programmatic Biological Opinion on the Effects 21 of Small Highway Projects on the Threatened Giant Garter Snake in Butte, 22 Colusa, Glenn, Sacramento, San Joaquin, Solano, Sutter, Yolo, Yuba Counties, 23 California. January 24.
24 USFWS 2010. U.S. Fish and Wildlife Service. Best Management Practices for Pacific 25 Lamprey. April.
26 Williams 2009. Williams, P.B., E. Andrews, J.J. Opperman, S. Bozkurt, and P.B. Moyle. 27 Quantifying activated floodplains on a lowland regulated river: its application to 28 floodplain restoration in the Sacramento Valley. San Francisco Estuary & 29 Watershed Science. September.
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Mendota Pool Bypass and Reach 2B Improvements Project Attachment A – Initial Alternatives Evaluation 10-3 – October 2012 San Joaquin River Restoration Program
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Mendota Pool Bypass and Reach 2B Improvements Project 10-4 – October 2012 Attachment A – Initial Alternatives Evaluation
Mendota Pool Bypass and Reach 2B Improvements Project
Project Description Technical Memorandum Attachment B – Evaluation Matrix
October 2012 SJRRP Reach 2B and Mendota Pool Bypass Evaluation Matrix Alternatives Evaluation Raw Data Attachment B
Initial Alternatives Floodplain Initial Alternatives Mendota Pool Bypass Initial Alternatives
P Settlement Compact Units of Fresno Slough Perspective Categories Factors Criteria or FP-1 FP-2 FP-3 FP-4 FP-5 Alignment Alignment Measure Dam N* Bypass Bypass A. Implementation/Technical Feasibility Capital Improvement Costs dollars N $194,430,000 $192,480,000 $194,780,000 $218,110,000 $266,900,000 $225,370,000 $234,970,000 $375,990,000 Upfront Costs Land Costs dollars N $15,300,000 $19,800,000 $19,800,000 $27,300,000 $36,300,000 $13,000,000 $7,000,000 $8,890,000 Costs Subtotal dollars N $209,730,000 $212,280,000 $214,580,000 $245,410,000 $303,200,000 $238,370,000 $241,970,000 $384,880,000 Long-Term Costs O&M dollars/year N $606,000 $646,000 $646,000 $721,000 $846,000 $500,000 $540,000 $666,000 Time to Build Timeline Time until action is functional months N 40 40 40 45 52 59 59 65 B. Objectives/Benefits Achievement rating: 1 Shallow Water Habitat Quality (poor), 3 P13321111 Floodplain (good) Characteristics Rearing habitat (>1.0 feet inundation acres P 373 482 481 585 762 58 -91 39 at 2,500 cfs) number of Passage Conditions Artificial structures in migratory path N2222210104 Fish Habitat & structures for Adult Chinook Passage number of Salmon Total number of steps at structures N1212121212212116 jumps number of Fish Screens along migratory path N11111111 Passage Conditions screens for Juvenile number of Chinook Salmon Potential predation sites at structures artificial N3333311115 structures Wetlands and other waters of the acres of hydric P 451.3 518.3 518.3 751.6 980.4 55.6 97.8 101.8 U.S area soils Sensitive vegetation alliance extent acres P 817.0 1208.1 1208.7 1752.2 2432.5 141.5 218.0 251.2
Button willow thickets acres P 36.8 70.9 43.0 167.2 240.4 0.0 0.0 0.0 California bulrush marsh acres P 46.9 72.2 72.2 72.2 76.5 0.0 68.5 0.0 California mugwort brush acres P 96.4 117.8 114.5 163.0 201.3 18.5 18.0 16.2 Vegetation Creeping rye grass turfs acres P 49.3 46.6 47.1 97.6 182.4 20.0 19.1 27.8 Riparian banks forbes and herbs acres P 89.5 90.9 117.1 89.0 86.4 61.1 42.4 41.4 Salt grass flats acres P 148.0 248.4 218.8 483.3 578.0 15.2 23.2 50.5 Fremont cottonwood forest acres P 14.6 38.9 38.6 51.1 198.9 0.0 0.0 0.0 Oregon ash groves acres P 35.7 67.2 61.8 63.5 118.3 0.0 0.0 0.0 Habitat Sandbar willow thickets acres P 124.9 261.9 277.0 318.7 423.8 13.7 1.0 23.1 Restoration Black willow thickets acres P 97.9 114.5 140.8 169.1 249.1 13.0 16.8 72.0 Exist. sensitive vegetation alliance acres P 76.9 78.7 77.6 77.5 77.3 0.0 15.7 20.3 preservation Wildlife habitat extent acres P 740.1 1129.4 1131.1 1674.7 2355.2 141.5 202.1 230.9 Freshwater emergent wetland acres P 136.4 163.2 189.4 161.2 163.0 61.1 110.8 41.4 Riparian scrub acres P 133.2 188.7 298.4 330.1 446.1 18.5 18.0 16.2 Valley foothill riparian acres P 50.3 106.1 100.4 114.6 326.5 0.0 0.0 0.0 Wet herbaceous acres P 197.4 295.1 265.9 580.9 746.7 35.2 43.9 78.3 Wildlife Willow scrub acres P 222.8 376.4 277.0 487.9 672.9 26.7 17.6 95.1 Special-status species habitat extent acres P 581.4 859.4 821.6 1437.6 1982.9 131.5 210.4 197.9
Greater sandhill crane acres P 333.8 458.2 455.3 742.1 909.7 96.3 162.0 119.6 Swainson's hawk acres P 247.6 401.2 366.3 695.5 1073.2 35.2 43.9 78.3 Net change in wildland extent acres P 395.6 756.3 756.9 1299.9 1979.0 188.1 155.9 72.6 Potential for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion dollars N $1,935,000 $1,123,000 $1,123,000 $315,000 $130,000 $8,455,000 $7,824,000 $2,306,000 protection cost) C. Impacts Acres of land in which groundwater levels rise above 5-foot monitoring acres N 490 330 330 300 230 0 0 0 threshold Groundwater Seepage Impacts Acres of land in which groundwater levels rise above 7-foot monitoring acres N 580 390 390 360 320 0 0 0 threshold Total Farmland Removed from acres N 400.5 658.7 658.7 1,159.2 1,797.1 717.8 158.3 389.1 Production Alfalfa acres N 0.0 0.0 0.0 0.0 0.0 190.2 41.2 68.7 Almond acres N 213.0 340.4 340.4 544.7 982.0 250.3 24.7 81.9 Socioeconomic Crop Acreage Grapes acres N 64.6 76.1 76.1 169.6 287.8 0.0 0.0 83.5 s and Other Row Crop acres N 0.0 0.0 0.0 0.0 0.0 277.3 92.4 167.5 Economics Palm acres N 9.7 9.7 9.7 9.7 9.7 0.0 0.0 0.0 Pistachio acres N 113.3 232.5 232.5 435.2 517.6 0.0 0.0 5.4 Agricultural Reduction in annual agricultural dollars N $2,339,259 $3,630,735 $3,630,735 $6,084,658 $8,988,212 $1,528,896 $265,460 $1,023,146 Economic Impacts production values Wetland Impacts acres N 66.4 64.6 66.8 62.9 64.2 15.5 24.2 30.4 Freshwater Emergent Wetland acres N 0.0 0.0 0.0 0.0 0.0 0.0 0.0 7.6 Freshwater Forested/Shrub Wetland acres N 41.3 40.4 40.6 40.1 40.2 11.8 9.4 10.0 Riverine acres N 25.1 24.1 26.2 22.8 24.0 3.7 14.9 12.8 Sensitive Vegetation Alliance Direct acres N 48.0 48.2 50.0 48.6 49.3 9.7 22.8 22.4 Impacts Alkali heath marsh acres N 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.4 Arrow weed thickets acres N 0.1 0.2 0.2 0.2 0.2 0.0 0.0 0.1 Black willow thickets acres N 19.9 18.5 19.1 18.1 18.0 0.7 11.6 8.9 Blue elderberry stands acres N 16.3 16.4 16.6 16.3 16.3 0.0 0.0 0.3 Special Status Button willow thickets acres N 0.1 0.1 0.2 0.1 0.1 0.0 0.0 0.3 Vegetation California bulrush marsh acres N 0.5 0.6 0.6 1.0 0.9 0.2 0.2 3.7 California rose briar patches acres N 4.4 4.4 4.6 4.4 4.4 0.0 1.0 2.5 Creeping rye grass turfs acres N 0.2 0.0 0.0 0.0 0.1 0.0 0.6 0.7 Fremont cottonwood forest acres N 3.6 3.0 3.1 3.8 4.2 8.8 8.9 4.6 Oregon ash groves acres N 0.9 0.9 1.5 0.8 0.8 0.0 0.1 0.1 Pale spike rush marshes acres N 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.3 Salt grass flats acres N 0.9 0.9 0.9 0.9 0.9 0.0 0.0 0.3 Silver bush lupine scrub acres N 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Spinescale scrub acres N 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.4 Environmental Tar plant fields acres N 1.0 3.1 3.1 2.9 3.2 0.0 0.2 0.7 Yerba mansa meadows acres N 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1
Special status wildlife habitat impacts acres N 211.1 192.1 194.7 189.7 190.4 186.9 156.9 220.0
Blunt-nosed leopard lizard acres N 11.5 11.1 11.1 10.9 11.3 0.0 0.0 0.0 Fairy shrimp acres N 2.3 2.3 2.3 2.3 2.3 0.0 0.0 0.0 Fresno kangaroo rat acres N 11.5 11.1 11.1 10.9 11.3 0.0 0.0 0.0 Special Status Giant garter snake acres N 35.0 37.2 39.1 38.9 39.8 3.4 18.3 44.9 Wildlife Greater sandhill crane acres N 56.0 52.2 52.2 48.4 46.1 120.9 101.3 127.0 San Joaquin kit fox acres N 30.4 24.1 24.1 24.2 24.6 0.0 0.0 12.4 Swainson's hawk acres N 48.0 37.7 38.2 37.9 38.6 62.6 37.4 35.4 Valley elderberry longhorn beetle acres N 16.3 16.4 16.6 16.3 16.3 0.0 0.0 0.3
number of Valley elderberry longhorn beetle N 270 273 285 270 271 0 0 15 elderberry shrubs number of Historic Properties Potentially listed N33333012 Cultural and Effected properties Historical ranking: 1 Resources Buried Deposits Sensitivity (very low)-5 N44444144 (very high)
O:\6000 Deliverables T2\6800 Project Description (T2.7)\[3] Final Public TM\Att A Alts Evaluation\Evaluation Matrix\Evaluation Matrix 20121005.xlsx 10/11/2012 SJRRP Reach 2B and Mendota Pool Bypass Evaluation Matrix Alternatives Evaluation Median Ratio Summary (Qual) Attachment B Initial Alternatives
Floodplain Initial Alternatives Mendota Pool Bypass Initial Alternatives
Settlement Alignment Compact Alignment FP-1 FP-2 FP-3 FP-4 FP-5 Fresno Slough Dam Bypass Bypass
Perspective P Categories Factors Criteria or N1 Factor Level Factor Level Factor Level Factor Level Factor Level Factor Level Factor Level Factor Level Criteria Level Criteria Level Criteria Level Criteria Level Criteria Level Criteria Level Criteria Level Criteria Level Category Level Category Level Category Level Category Level Category Level Category Level Category Level Category Level Perspective Level Perspective Level Perspective Level Perspective Level Perspective Level Perspective Level Perspective Level Perspective Level A. Implementation/Technical Feasibility Capital Improvement Costs N med med med med low med med low Upfront Costs med med med med low med high med Costs Land Costs N medmed medmed medmed lowmed lowlow lowmed medmed med low med med med med low med med low Long-Term Costs O&M N med med med med med med med med low low med med med med low low Time to Build Timeline Time until action is functional N med med med med med med med med med low low low low low low med med med med med med low low low B. Objectives/Benefits Achievement Shallow Water Habitat Quality P low high high med low low low low Floodplain CharacteristicsRearing habitat (>1.0 feet inundation low med med med med med low med P med med med med high med low med at 2,500 cfs)
Artificial structures in migratory path N low low low low low med med high Passage Conditions for Fish Habitat & Passage lowlow lowmed lowmed lowmed low med medmed med low high high Adult Chinook Salmon Total number of steps at structures N low low low low low med med high Fish Screens along migratory path N low low low low low low low low Passage Conditions for Potential predation sites at low low low low low med med high Juvenile Chinook Salmon N low low low low low med med high structures low med med high high med med high Wetlands and other waters of the P med med med high high low med med U.S area Vegetation med med med high high low med med Sensitive vegetation alliance extent P low high med med med low med med Habitat Restoration med med med high high low med med Wildlife habitat extent P med med med high high low med med WildlifeSpecial-status species habitat extent P med med med med med med high high high high lowmed med high med med Net change in wildland extent P med med med high high med med low Potential for lateral migration to Geomorphology Channel Stability impact levees (estimated erosion N low low low med med med med med med high high high high high high med med med med med med high high high protection cost) C. Impacts Acres of land in which groundwater levels rise above 5-foot monitoring N low med med med high threshold Groundwater Seepage Impacts low low med med med med med med med med Acres of land in which groundwater levels rise above 7-foot monitoring N low med med med med threshold Total Farmland Removed from Land Use Crop Acreage N med med med med med med med med med low low low low low low low low low high high high med med med Production Agricultural Economic Change in annual agricultural Socioeconomics and Economics N med med medmed med med medmed med med medmed low low lowlow low low lowlow med med med med high high highhigh med med med med Impacts production values Wetland Impacts N low med low high med high med low Special Status VegetationSensitive Vegetation Alliance Direct med med low high med high med med N med med low med med high med med Impacts Special status wildlife habitat Environmental Special Status Wildlife N low lowlow med medmed med medlow med medmed med medmed med medhigh high highmed low low low impacts Historic Properties Potentially Cultural and Historical N low low low low low high med low Effected low low low low low high med med Resources Buried Deposits Sensitivity N low low low low low high med med TOTAL2 low low med low med med high med med med high med med med med med med med low low med low low low high high med high med med med med Notes: 1 P or N refers to whether higher raw data values constitute positive or negative outcomes. If P, then high raw data values get normalized to high scores. If N, then high raw data values get normalized to low scores 2 Totals reflect all criteria, factors, categories, and perspectives. Totals are rated according to their distribution amongst all the totals at a particular level for a particular set of alternatives. Blank cells indicate no data available or criteria ia not applicable to that set of alternatives.
O:\6000 Deliverables T2\6800 Project Description (T2.7)\[3] Final Public TM\Att A Alts Evaluation\Evaluation Matrix\Evaluation Matrix 20121005.xlsx 10/11/2012 SJRRP Reach 2B and Mendota Pool Bypass Evaluation Matrix Alternatives Evaluation Summary Chart Attachment B Summary of Total Scores
FP-1 FP-2 FP-3 FP-4 FP-5 Settlement Compact Fresno Slough Alignment Bypass Alignment Bypass Dam Implementation/Technical Feasibility Objectives/Benefits Achievement Impacts
O:\6000 Deliverables T2\6800 Project Description (T2.7)\[3] Final Public TM\Att A Alts Evaluation\Evaluation Matrix\Evaluation Matrix 20121005.xlsx 10/11/2012